03 Mar '10
details: http://www.bx.psu.edu/hg/galaxy/rev/0291f870f2c9
changeset: 3470:0291f870f2c9
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Wed Mar 03 13:40:26 2010 -0500
description:
Error conditions will skip lines instead of stopping the tool for the lastz paired reads, and clean up the tool pages for both lastz tools.
diffstat:
tools/sr_mapping/lastz_paired_reads_wrapper.py | 134 ++++++++++++++++++-----
tools/sr_mapping/lastz_paired_reads_wrapper.xml | 102 +-----------------
tools/sr_mapping/lastz_wrapper.xml | 18 +-
3 files changed, 118 insertions(+), 136 deletions(-)
diffs (464 lines):
diff -r 8e9aa1709c6c -r 0291f870f2c9 tools/sr_mapping/lastz_paired_reads_wrapper.py
--- a/tools/sr_mapping/lastz_paired_reads_wrapper.py Wed Mar 03 12:07:39 2010 -0500
+++ b/tools/sr_mapping/lastz_paired_reads_wrapper.py Wed Mar 03 13:40:26 2010 -0500
@@ -78,11 +78,49 @@
# Keep track of all created temporary files so they can be deleted
global tmp_file_names
tmp_file_names = []
+# The values in the skipped_lines dict are tuples consisting of:
+# - the number of skipped lines for that error
+# If not a sequence error:
+# - the 1st line number on which the error was found
+# - the text of the 1st line on which the error was found
+# If a sequence error:
+# - The number of the sequence in the file
+# - the sequence name on which the error occurred
+# We may need to improve dealing with file position and text as
+# much of it comes from temporary files that are created from the
+# inputs, and not the inputs themselves, so this could be confusing
+# to the user.
+global skipped_lines
+skipped_lines = dict( bad_interval=( 0, 0, '' ),
+ inconsistent_read_lengths=( 0, 0, '' ),
+ inconsistent_reads=( 0, 0, '' ),
+ inconsistent_sizes=( 0, 0, '' ),
+ missing_mate=( 0, 0, '' ),
+ missing_quals=( 0, 0, '' ),
+ missing_seq=( 0, 0, '' ),
+ multiple_seqs=( 0, 0, '' ),
+ no_header=( 0, 0, '' ),
+ num_fields=( 0, 0, '' ),
+ reads_paired=( 0, 0, '' ),
+ sam_flag=( 0, 0, '' ),
+ sam_headers=( 0, 0, '' ),
+ sam_min_columns=( 0, 0, '' ),
+ two_mate_names=( 0, 0, '' ),
+ wrong_seq_len=( 0, 0, '' ) )
+global total_skipped_lines
+total_skipped_lines = 0
def stop_err( msg ):
sys.stderr.write( "%s" % msg )
sys.exit()
+def skip_line( error_key, position, text ):
+ if not skipped_lines[ error_key ][2]:
+ skipped_lines[ error_key ][1] = position
+ skipped_lines[ error_key ][2] = text
+ skipped_lines[ error_key ][0] += 1
+ total_skipped_lines += 1
+
def get_tmp_file_name( dir=None, suffix=None ):
"""
Return a unique temporary file name that can be managed. The
@@ -150,16 +188,16 @@
line = line.split( "#", 1 )[0].rstrip()
fields = line.split()
if len( fields ) != 4:
- # TODO: Do we want to err out here or just skip the line?
- stop_err( "Wrong number of fields ( must be 4 ) in line %d: %s" % ( i+1, line ) )
+ skip_line( 'num_fields', i+1, line )
+ continue
name, start, length, size = fields
start = int( start )
length = int( length )
size = int( size )
end = start + length
if end > size:
- # TODO: Do we want to err out here or just skip the line?
- stop_err( "Bad interval in line %d: %s" % ( i+1, line ) )
+ skip_line[ 'bad_interval' ] += 1
+ continue
if name not in read_to_linker_dict:
read_to_linker_dict[ name ] = ( start, end, size )
continue
@@ -168,9 +206,8 @@
continue
( s, e, sz ) = read_to_linker_dict[ name ]
if sz != size:
- # This should never occur
- # TODO: Do we want to err out here or just skip the line?
- stop_err( "Inconsistent sizes for %s" % name )
+ skip_line( 'inconsistent_sizes', i+1, name )
+ continue
if s > end or e < start:
# Non-overlapping intervals, so skip this sequence
read_to_linker_dict[ name ] = None
@@ -194,18 +231,15 @@
read_to_linker_dict[ seq.name ] = ""
continue
if read_to_linker_dict[ seq.name ] == "":
- # TODO: Do we want to err out here or just skip the line?
- stop_err( "Multiple sequences named %s" % seq.name )
+ skip_line( 'multiple_seqs', seqs, seq.name )
+ continue
if read_to_linker_dict[ seq.name ] == None:
# Read previously marked as non-overlapping intervals, so skip this sequence - see above
continue
( start, end, size ) = read_to_linker_dict[ seq.name ]
if seq.length != size:
- # TODO: Do we want to err out here or just skip the line?
- combined_linker_file.close()
- mates_file.close()
- mates_mapping_file.close()
- stop_err( "Sequence disagrees with size for sequence %s, size: %s seq.length: %s" % ( seq.name, str( size ), str( seq.length ) ) )
+ skip_line( 'wrong_seq_len', seqs, seq.name )
+ continue
left = seq.text[ :start ]
right = seq.text[ end: ]
left_is_small = len( left ) <= seq_len_lower_threshold
@@ -272,7 +306,9 @@
if not seq:
break
seqs += 1
- # Create a temporary file to contain the current sequence as input to lastz
+ # Create a temporary file to contain the current sequence as input to lastz.
+ # We're doing this a bit differently here since we could be generating a huge
+ # number of temporary files.
tmp_in_fd, tmp_in_file_name = tempfile.mkstemp( suffix='seq_%d_in' % seqs )
tmp_in_file = os.fdopen( tmp_in_fd, 'w+b' )
tmp_in_file.write( '>%s\n%s\n' % ( seq.name, seq.text ) )
@@ -441,10 +477,12 @@
if not line.startswith( "#" ):
fields = line.split()
if len( fields ) != 4:
- stop_err( "Incorrect number of fields (must be 4) in line %s of file %s" % ( i+1, tmp_mates_mapping_file_name ) )
+ skip_line( "num_fields", i+1, line )
+ continue
mate_name, read_name, s_offset, e_offset = fields
if mate_name in mate_to_read_dict:
- stop_err( "%s is in the mate_to_read_dict when it should not be." % mate_name )
+ skip_line( 'two_mate_names', i+1, mate_name )
+ continue
mate_to_read_dict[ mate_name ] = ( read_name, int( s_offset ), int( e_offset ) )
# Read sequence data
read_to_nucs_dict = {}
@@ -458,9 +496,8 @@
seq_text_upper = seq.text.upper()
if seq.name in read_to_nucs_dict:
if seq_text_upper != read_to_nucs_dict[ seq.name ]:
- # TODO: Should we err out here or just skip the line?
- stop_err( "Inconsistent reads named %s (second occurs at line %d in file %s)" % ( seq.name, seqs, input2 ) )
- #continue
+ skip_line( 'inconsistent_reads', seqs, seq.name )
+ continue
read_to_nucs_dict[ seq.name ] = seq_text_upper
# Read quality data
def quality_sequences( f ):
@@ -477,7 +514,8 @@
seq_line = line_number
seq_quals = []
elif seq_name is None:
- stop_err( "First quality sequence has no header" )
+ skip_line( 'no_header', line_number, line )
+ continue
else:
seq_quals += [ int( q ) for q in line.split() ]
if seq_name is not None:
@@ -494,11 +532,11 @@
quals = samify_phred_scores( quals )
if seq_name in read_to_quals_dict:
if quals != read_to_quals_dict[ seq_name ]:
- stop_err( "Inconsistent quality sequences named %s (second occurs at line %d in %s)" % ( seq_name, line_number, input4 ) )
+ skip_line( 'inconsistent_reads', line_number, seq_name )
continue
if len( quals ) != len( read_to_nucs_dict[ seq_name ] ):
- stop_err( "Inconsistent read/quality lengths for %s, quals: %s, read_to_nucs_dict[ seq_name ]: %s" % \
- ( seq_name, quals, read_to_nucs_dict[ seq_name ] ) )
+ skip_line( 'inconsistent_read_lengths', line_number, seq_name )
+ continue
read_to_quals_dict[ seq_name ] = quals
# process the SAM file
tmp_align_file_names = ' '.join( tmp_align_file_name_list )
@@ -512,21 +550,25 @@
line = line.strip()
if line.startswith( "@" ):
if has_non_header:
- stop_err( "Input SAM contains headers in several places (e.g., line %d) in file %s" % ( i+1, combined_chrom_file_name ) )
+ skip_line( 'sam_headers', i+1, line )
+ continue
fout.write( "%s\n" % line )
continue
has_non_header = True
fields = line.split()
num_fields = len( fields )
if num_fields < SAM_MIN_COLUMNS:
- stop_err( "Not enough columns at line %d (%d, expected %d)" % ( i+1, num_fields, SAM_MIN_COLUMNS ) )
+ skip_line( 'sam_min_columns', i+1, line )
+ continue
# Set flags for mates
try:
flag = int( fields[ SAM_FLAG_COLUMN ] )
except ValueError:
- stop_err( "Bad SAM flag at line %d: %s" % ( i+1, line ) )
+ skip_line( 'sam_flag', i+1, line )
+ continue
if not( flag & ( BAM_FPAIRED + BAM_FREAD1 + BAM_FREAD2 ) == 0 ):
- stop_err( "SAM flag indicates reads already paired, at line %d\n%s" % ( i+1, line ) )
+ skip_line( 'reads_paired', i+1, line )
+ continue
mate_name = fields[ SAM_QNAME_COLUMN ]
unmap_it = False
half = None
@@ -548,7 +590,8 @@
try:
read_name, s_offset, e_offset = mate_to_read_dict[ mate_name ]
except KeyError:
- stop_err( "'%s' doesn't appear in the mapping file." % mate_name )
+ skip_line( 'missing_mate', i+1, mate_name )
+ continue
cigar = fields[ SAM_CIGAR_COLUMN ]
cigar_prefix = None
cigar_suffix = None
@@ -598,14 +641,16 @@
fields[ SAM_CIGAR_COLUMN ] = cigar
# Fetch sequence and quality values, and flip/clip them
if read_name not in read_to_nucs_dict:
- stop_err( "Missing sequence for '%s'" % read_name )
+ skip_line( 'missing_seq', i+1, read_name )
+ continue
nucs = read_to_nucs_dict[ read_name ]
if not on_plus_strand:
nucs = reverse_complement( nucs )
quals = None
if read_to_quals_dict != None:
if read_name not in read_to_quals_dict:
- stop_err( "Missing quality values for '%s'" % read_name )
+ skip_line( 'missing_quals', i+1, read_name )
+ continue
quals = read_to_quals_dict[ read_name ]
if not on_plus_strand:
quals = reverse_string( quals )
@@ -752,5 +797,32 @@
# Delete all temporary files
for file_name in tmp_file_names:
os.remove( file_name )
+ # Handle any invalid lines in the input data
+ if total_skipped_lines:
+ msgs = dict( bad_interval="Bad interval in line",
+ inconsistent_read_lengths="Inconsistent read/quality lengths for seq #",
+ inconsistent_reads="Inconsistent reads for seq #",
+ inconsistent_sizes="Inconsistent sizes for seq #",
+ missing_mate="Mapping file does not include mate on line",
+ missing_quals="Missing quality values for name on line",
+ missing_seq="Missing sequence for name on line",
+ multiple_seqs="Multiple names for seq #",
+ no_header="First quality sequence has no header",
+ num_fields="Must have 4 fields in line",
+ reads_paired="SAM flag indicates reads already paired on line",
+ sam_flag="Bad SAM flag on line",
+ sam_headers="SAM headers on line",
+ sam_min_columns="Need 11 columns on line",
+ two_mate_names="Mate name already seen, line",
+ wrong_seq_len="Size differs from length of seq #" )
+ print "Skipped %d invalid lines: "
+ msg = ""
+ for k, v in skipped_lines.items():
+ if v[0]:
+ # v[0] is the number of times the error occurred
+ # v[1] is the position of the line or sequence in the file
+ # v[2] is the name of the sequence or the text of the line
+ msg += "(%d)%s %d:%s. " % ( v[0], msgs[k], v[1], v[2] )
+ print msg
if __name__=="__main__": __main__()
diff -r 8e9aa1709c6c -r 0291f870f2c9 tools/sr_mapping/lastz_paired_reads_wrapper.xml
--- a/tools/sr_mapping/lastz_paired_reads_wrapper.xml Wed Mar 03 12:07:39 2010 -0500
+++ b/tools/sr_mapping/lastz_paired_reads_wrapper.xml Wed Mar 03 13:40:26 2010 -0500
@@ -38,7 +38,7 @@
<param name="input3" format="fasta" type="data" label="Linker file" />
<param name="input4" format="qual454" type="data" label="Select a base quality score 454 dataset" />
<conditional name="seq_name">
- <param name="how_to_name" type="select" label="Do you want to modify reference name?">
+ <param name="how_to_name" type="select" label="Do you want to modify the reference name?">
<option value="no">No</option>
<option value="yes">Yes</option>
</param>
@@ -75,9 +75,9 @@
**What it does**
-**LASTZ** is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. Special scoring sets were derived to improve runtime performance and quality. The Galaxy version of LASTZ is geared towards aligning of short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence. There is excellent, extensive `documentation`__ on LASTZ available, although it hasn't been updated for the version of LASTZ that Galaxy is running (the key changes have to do with output formats, so it is still extremely helpful).
+**LASTZ** is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. Special scoring sets were derived to improve runtime performance and quality. This Galaxy version of LASTZ is geared towards aligning short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) paired reads against a reference sequence. There is excellent, extensive documentation on LASTZ available here_.
- .. __: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.01.50/README.lastz-1.0…
+ .. _here: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.0…
------
@@ -89,7 +89,7 @@
**Outputs**
-LASTZ generates one output. Depending on the choice you make in *Select output format* drop-down LASTZ will produce a SAM file showing sequence alignments, a list of differences between the reads and reference (Polymorphisms), or a general table with one line per alignment block (Tabular). Examples of these outputs are shown below.
+This LASTZ tool produces a SAM file showing sequence alignments.
**SAM output**
@@ -132,102 +132,11 @@
0x0080 the read is the second read in a pair
0x0100 the alignment is not primary
-**Polymorphism (SNP or differences) output**
-
-Polymorphism output contains 14 columns::
-
- 1 2 3 4 5 6 7 8 9 10 11 12 13 14
- --------------------------------------------------------------------------------------------------------------------------------------------------------------
- chrM 2490 2491 + 5386 HWI-EAS91_1_306UPAAXX:6:1:486:822 10 11 - 36 C A ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC
- chrM 2173 2174 + 5386 HWI-EAS91_1_306UPAAXX:6:1:259:1389 26 27 + 36 G T GCGTACTTATTCGCCACCATGATTATGACCAGTGTT GCGTACTTATTCGCCACCATGATTATTACCAGTGTT
-
-where::
-
- 1. (chrM) - Reference sequence id
- 2. (2490) - Start position of the difference in the reference
- 3. (2491) - End position of the difference in the reference
- 4. (+) - Strand of the reference (always plus)
- 5. (5386) - Length of the reference sequence
- 6. (HWI...) - read id
- 7. (10) - Start position of the difference in the read
- 8. (11) - End position of the difference in the read
- 9. (+) - Strand of the read
- 10. (36) - Length of the read
- 11. (C) - Nucleotide in the reference
- 12. (A) - Nucleotide in the read
- 13. (ACC...) - Reference side os the alignment
- 14. (ACC...) - Read side of the alignment
-
-**Tabular output**
-
-Tabular output is a tab-separated format with 30 columns::
-
- 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
- -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
- 14 PHIX174 + 5386 4648 4647 4661 14 ATTTTCGTGATATT EYKX4VC01BV8HS + 204 154 153 167 154 153 167 14 ATTTTCGTGATATT .............. 14M 14/14 100.0% 14/204 6.9% 0/14 0.0% 4494 NA
- 16 PHIX174 + 5386 3363 3362 3378 16 GACGCCGGATTTGAGA EYKX4VC01AWJ88 - 259 36 35 51 209 208 224 16 GACGCCGGATTTGAGA ................ 16M 16/16 100.0% 16/259 6.2% 0/16 0.0% 3327 NA
-
-The following columns are present::
-
- Field Meaning
- ---------------- -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
- 1. score Score of the alignment block. The scale and meaning of this number will vary, depending on the final stage performed and other command-line options.
- 2. name1 Name of the target sequence.
- 3. strand1 Target sequence strand, either "+" or "−".
- 4. size1 Size of the entire target sequence.
- 5. start1 Starting position of the alignment block in the target, origin-one.
- 6. zstart1 Starting position of the alignment block in the target, origin-zero.
- 7. end1 Ending position of the alignment block in the target, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems).
- 8. length1 Length of the alignment block in the target (excluding gaps).
- 9. text1 Aligned characters in the target, including gap characters.
- 10. name2 Name of the query sequence.
- 11. strand2 Query sequence strand, either "+" or "−".
- 12. size2 Size of the entire query sequence.
- 13. start2 Starting position of the alignment block in the query, origin-one.
- 14. zstart2 Starting position of the alignment block in the query, origin-zero.
- 15. end2 Ending position of the alignment block in the query, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems).
- 16. start2+ Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-one. Note that if strand2 is "−", then this is the other end of the block from start2.
- 17. zstart2+ Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-zero. Note that if strand2 is "−", then this is the other end of the block from zstart2.
- 18. end2+ Ending position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems). Note that if strand2 is "−", then this is the other end of the block from end2.
- 19. length2 Length of the alignment block in the query (excluding gaps).
- 20. text2 Aligned characters in the query, including gap characters.
- 21. diff Differences between what would be written for text1 and text2. Matches are written as . (period), transitions as : (colon), transversions as X, and gaps as - (hyphen).
- 22. cigar A CIGAR-like representation of the alignment's path through the Dynamic Programming matrix. This is the short representation, without spaces, described in the Ensembl CIGAR specification.
- 23./24. identity Fraction of aligned bases in the block that are matches (see Identity). This is written as two fields. The first field is a fraction, written as <n>/<d>. The second field contains the same value, computed as a percentage.
- 25./26. coverage Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (see Coverage). This is written as two fields. The first field is a fraction, written as <n>/<d>. The second field contains the same value, computed as a percentage.
- 27./28. gaprate Rate of gaps (also called indels) in the alignment block. This is written as two fields. The first field is a fraction, written as <n>/<d>, with the numerator being the number of alignment columns containing gaps and the denominator being the number without gaps. The second field contains the same value, computed as a percentage.
- 29. diagonal The diagonal of the start of the alignment block in the dynamic programming matrix, expressed as an identifying number start1-start2.
- 30. shingle A measurement of the shingle overlap between the target and the query. This is intended for the case where both the target and query are relatively short, and their ends are expected to overlap.
-
--------
-
-**LASTZ Settings**
-
-There are two setting modes: (1) **Commonly used settings** and (2) **Full Parameter List**.
-
-**Commonly used settings**
-
-There are seven modes::
-
- Illumina-Solexa/AB-SOLiD 95% identity
- Illumina-Solexa/AB-SOLiD 85% identity
- Roche-454 98% identity
- Roche-454 95% identity
- Roche-454 90% identity
- Roche-454 85% identity
- Roche-454 75% identity
-
-when deciding which one to use consider the following: a 36 bp read with two difference will be 34/36 = 94% identical to the reference.
-
-**Full Parameter List**
-
-This modes gives you a fuller control over lastz. The description of these and other parameters is found at the end of this page. Note, that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs(a)bx.psu.edu.
-
------
-**Do you want to modify reference name?**
+**Do you want to modify the reference name?**
-This option allows you set the name of the reference sequence manually. This is helpful when, for example, you would like to make reference name compatible with the UCSC naming conventions to be able to display your lastz results as a custom track at UCSC Genome Browser.
+This option allows you to set the name of the reference sequence manually. This is helpful when, for example, you would like to make the reference name compatible with the UCSC naming conventions to be able to display your lastz results as a custom track at the UCSC Genome Browser.
------
diff -r 8e9aa1709c6c -r 0291f870f2c9 tools/sr_mapping/lastz_wrapper.xml
--- a/tools/sr_mapping/lastz_wrapper.xml Wed Mar 03 12:07:39 2010 -0500
+++ b/tools/sr_mapping/lastz_wrapper.xml Wed Mar 03 13:40:26 2010 -0500
@@ -97,7 +97,7 @@
</when>
</conditional>
<conditional name="seq_name">
- <param name="how_to_name" type="select" label="Do you want to modify reference name?">
+ <param name="how_to_name" type="select" label="Do you want to modify the reference name?">
<option value="no">No</option>
<option value="yes">Yes</option>
</param>
@@ -213,9 +213,9 @@
**What it does**
-**LASTZ** is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. Special scoring sets were derived to improve runtime performance and quality. The Galaxy version of LASTZ is geared towards aligning of short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence. There is excellent, extensive `documentation`__ on LASTZ available, although it hasn't been updated for the version of LASTZ that Galaxy is running (the key changes have to do with output formats, so it is still extremely helpful).
+**LASTZ** is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. Special scoring sets were derived to improve runtime performance and quality. This Galaxy version of LASTZ is geared towards aligning short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence. There is excellent, extensive documentation on LASTZ available here_.
- .. __: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.01.50/README.lastz-1.0…
+ .. _here: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.0…
------
@@ -227,7 +227,7 @@
**Outputs**
-LASTZ generates one output. Depending on the choice you make in *Select output format* drop-down LASTZ will produce a SAM file showing sequence alignments, a list of differences between the reads and reference (Polymorphisms), or a general table with one line per alignment block (Tabular). Examples of these outputs are shown below.
+LASTZ generates one output. Depending on the choice you make in the *Select output format* drop-down, LASTZ will produce a SAM file showing sequence alignments, a list of differences between the reads and reference (Polymorphisms), or a general table with one line per alignment block (Tabular). Examples of these outputs are shown below.
**SAM output**
@@ -355,23 +355,23 @@
Roche-454 85% identity
Roche-454 75% identity
-when deciding which one to use consider the following: a 36 bp read with two difference will be 34/36 = 94% identical to the reference.
+When deciding which one to use, consider the following: a 36 bp read with two differences will be 34/36 = 94% identical to the reference.
**Full Parameter List**
-This modes gives you a fuller control over lastz. The description of these and other parameters is found at the end of this page. Note, that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs(a)bx.psu.edu.
+This mode gives you fuller control over lastz. The description of these and other parameters is found at the end of this page. Note that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs(a)bx.psu.edu.
------
-**Do you want to modify reference name?**
+**Do you want to modify the reference name?**
-This option allows you set the name of the reference sequence manually. This is helpful when, for example, you would like to make reference name compatible with the UCSC naming conventions to be able to display your lastz results as a custom track at UCSC Genome Browser.
+This option allows you to set the name of the reference sequence manually. This is helpful when, for example, you would like to make the reference name compatible with the UCSC naming conventions to be able to display your lastz results as a custom track at the UCSC Genome Browser.
------
**LASTZ parameter list**
-This is an exhaustive list of LASTZ options. Once again, please note that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs(a)bx.psu.edu::
+This is an exhaustive list of LASTZ options. Once again, please note that not all options are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs(a)bx.psu.edu::
target[[s..e]][-] spec/file containing target sequence (fasta or nib)
[s..e] defines a subrange of the file
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/8e9aa1709c6c
changeset: 3469:8e9aa1709c6c
user: rc
date: Wed Mar 03 12:07:39 2010 -0500
description:
lims:
- Fixed a bug in saving the data folder for dataset transfer
- UI tweaks
- renamed request state 'Submitted' to 'In Progress'
diffstat:
lib/galaxy/model/__init__.py | 11 +++-
lib/galaxy/web/controllers/requests.py | 2 +-
lib/galaxy/web/controllers/requests_admin.py | 7 +-
templates/admin/requests/get_data.mako | 28 ++++++-----
templates/admin/requests/show_request.mako | 28 +++++------
templates/requests/show_request.mako | 67 +++++++++++++--------------
6 files changed, 74 insertions(+), 69 deletions(-)
diffs (283 lines):
diff -r bb7c2b314e3e -r 8e9aa1709c6c lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py Tue Mar 02 16:40:40 2010 -0500
+++ b/lib/galaxy/model/__init__.py Wed Mar 03 12:07:39 2010 -0500
@@ -1348,9 +1348,9 @@
class Request( object ):
states = Bunch( NEW = 'New',
- SUBMITTED = 'Submitted',
+ SUBMITTED = 'In Progress',
REJECTED = 'Rejected',
- COMPLETE = 'Complete')
+ COMPLETE = 'Complete' )
def __init__(self, name=None, desc=None, request_type=None, user=None,
form_values=None):
self.name = name
@@ -1385,6 +1385,7 @@
return self.state() == self.states.NEW
def complete(self):
return self.state() == self.states.COMPLETE
+
class RequestEvent( object ):
def __init__(self, request=None, request_state=None, comment=''):
@@ -1432,6 +1433,12 @@
if status == self.transfer_status.IN_PROGRESS:
count = count + 1
return count
+ def transferred_dataset_files(self):
+ count = 0
+ for df, status in self.dataset_files:
+ if status == self.transfer_status.COMPLETE:
+ count = count + 1
+ return count
class SampleState( object ):
def __init__(self, name=None, desc=None, request_type=None):
diff -r bb7c2b314e3e -r 8e9aa1709c6c lib/galaxy/web/controllers/requests.py
--- a/lib/galaxy/web/controllers/requests.py Tue Mar 02 16:40:40 2010 -0500
+++ b/lib/galaxy/web/controllers/requests.py Wed Mar 03 12:07:39 2010 -0500
@@ -947,7 +947,7 @@
msg=msg,
id=trans.security.encode_id(request.id) ))
# change the request state to 'Submitted'
- comments = "Request moved to 'Submitted' state."
+ comments = "Sequencing request is in progress."
event = trans.app.model.RequestEvent(request, request.states.SUBMITTED, comments)
trans.sa_session.add( event )
trans.sa_session.flush()
diff -r bb7c2b314e3e -r 8e9aa1709c6c lib/galaxy/web/controllers/requests_admin.py
--- a/lib/galaxy/web/controllers/requests_admin.py Tue Mar 02 16:40:40 2010 -0500
+++ b/lib/galaxy/web/controllers/requests_admin.py Wed Mar 03 12:07:39 2010 -0500
@@ -412,7 +412,7 @@
id=trans.security.encode_id(request.id) ) )
# change the request state to 'Submitted'
if request.user.email is not trans.user:
- comments = "Request moved to 'Submitted' state by admin (%s) on behalf of %s." % (trans.user.email, request.user.email)
+ comments = "Request submitted by admin (%s) on behalf of %s." % (trans.user.email, request.user.email)
else:
comments = ""
event = trans.app.model.RequestEvent(request, request.states.SUBMITTED, comments)
@@ -1295,8 +1295,6 @@
event = trans.app.model.RequestEvent(request, request.states.COMPLETE, comments)
trans.sa_session.add( event )
trans.sa_session.flush()
-# trans.sa_session.add( request )
-# trans.sa_session.flush()
def change_state(self, trans, sample):
possible_states = sample.request.type.states
curr_state = sample.current_state()
@@ -1775,7 +1773,8 @@
# data transfer info
rt.datatx_info = dict(host=util.restore_text( params.get( 'host', '' ) ),
username=util.restore_text( params.get( 'username', '' ) ),
- password=params.get( 'password', '' ))
+ password=params.get( 'password', '' ),
+ data_dir=util.restore_text( params.get( 'data_dir', '' ) ))
trans.sa_session.add( rt )
trans.sa_session.flush()
# set sample states
diff -r bb7c2b314e3e -r 8e9aa1709c6c templates/admin/requests/get_data.mako
--- a/templates/admin/requests/get_data.mako Tue Mar 02 16:40:40 2010 -0500
+++ b/templates/admin/requests/get_data.mako Wed Mar 03 12:07:39 2010 -0500
@@ -30,12 +30,6 @@
<h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3>
<ul class="manage-table-actions">
-## %if sample.request.submitted() and sample.untransferred_dataset_files():
-## <li>
-## <a class="action-button" href="${h.url_for( controller='requests_admin', action='start_datatx', id=trans.security.encode_id(sample.id) )}">
-## <span>Start data transfer</span></a>
-## </li>
-## %endif
%if sample.request.submitted() and sample.inprogress_dataset_files():
<li>
<a class="action-button" href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">
@@ -47,7 +41,7 @@
<span>Sequencer information</span></a>
</li>
<li>
- <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( sample.library.id ) )}">
+ <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=trans.security.encode_id( sample.library.id ) )}">
<span>${sample.library.name} Data Library</span></a>
</li>
<li>
@@ -57,17 +51,16 @@
</ul>
<div class="toolForm">
- <form name="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
- %if len(dataset_files):
+ %if len(dataset_files):
+## <form name="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
<div class="form-row">
- <h4>Datasets Transferred</h4>
+ <h4>Sample Dataset(s)</h4>
<div class="form-row">
<table class="grid">
<thead>
<tr>
<th>Dataset File</th>
<th>Transfer Status</th>
- ##<th>Data Library</th>
<th></th>
</tr>
<thead>
@@ -79,8 +72,14 @@
</table>
</div>
</div>
- %endif
+## </form>
+##</div>
+<br/>
+%endif
+##<div class="toolForm">
+ <form name="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
<div class="form-row">
+ ##<div class="toolFormTitle">Select files for transfer</div>
<h4>Select files for transfer</h4>
<div style="width: 60%;">
<div class="form-row">
@@ -98,6 +97,11 @@
</select>
</div>
<div class="form-row">
+ <div class="toolParamHelp" style="clear: both;">
+ After clicking <b>Transfer</b> do <i>not</i> close this page or
+ navigate away from this page. Once the transfer is complete
+ the dataset(s) will show up on this page.
+ </div>
<input type="submit" name="start_transfer_button" value="Transfer"/>
</div>
</div>
diff -r bb7c2b314e3e -r 8e9aa1709c6c templates/admin/requests/show_request.mako
--- a/templates/admin/requests/show_request.mako Tue Mar 02 16:40:40 2010 -0500
+++ b/templates/admin/requests/show_request.mako Wed Mar 03 12:07:39 2010 -0500
@@ -362,29 +362,27 @@
<table class="grid">
<tbody>
<tr>
- %if not request.complete():
<div class="form-row">
<td>
- %if current_samples and not request.complete():
+ %if current_samples:
<input type="submit" name="edit_samples_button" value="Edit samples"/>
%endif
</td>
%if request.unsubmitted():
- <td>
- <label>Import from csv file</label>
- <input type="file" name="file_data" />
- <input type="submit" name="import_samples_button" value="Import samples"/>
- </td>
- <td>
- %if current_samples:
- <label>Copy from sample</label>
- ${sample_copy.get_html()}
- %endif
- <input type="submit" name="add_sample_button" value="Add New"/>
- </td>
+ <td>
+ <label>Import from csv file</label>
+ <input type="file" name="file_data" />
+ <input type="submit" name="import_samples_button" value="Import samples"/>
+ </td>
+ <td>
+ %if current_samples:
+ <label>Copy from sample</label>
+ ${sample_copy.get_html()}
+ %endif
+ <input type="submit" name="add_sample_button" value="Add New"/>
+ </td>
%endif
</div>
- %endif
</tr>
</tbody>
</table>
diff -r bb7c2b314e3e -r 8e9aa1709c6c templates/requests/show_request.mako
--- a/templates/requests/show_request.mako Tue Mar 02 16:40:40 2010 -0500
+++ b/templates/requests/show_request.mako Wed Mar 03 12:07:39 2010 -0500
@@ -237,40 +237,6 @@
%endfor
</%def>
-<div class="toolForm">
- <div class="form-row">
- <div class="msg_list">
- <h4 class="msg_head"><u>Request Information</u></h4>
- <div class="msg_body">
- %for index, rd in enumerate(request_details):
- <div class="form-row">
- <label>${rd['label']}</label>
- %if not rd['value']:
- <i>None</i>
- %else:
- %if rd['label'] == 'State':
- <a href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}">${rd['value']}</a>
- %else:
- ${rd['value']}
- %endif
- %endif
- </div>
- <div style="clear: both"></div>
- %endfor
- <div class="form-row">
- <ul class="manage-table-actions">
- <li>
- <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='Edit', id=trans.security.encode_id(request.id))}">
- <span>Edit request details</span></a>
- </li>
- </ul>
- </div>
- </div>
- </div>
- </div>
-</div>
-<br/>
-
<%def name="render_grid( grid_index, grid_name, fields_dict )">
<br/>
<div class="msg_list">
@@ -325,7 +291,38 @@
</%def>
<div class="toolForm">
- ##<div class="toolFormTitle">Samples (${len(request.samples)})</div>
+ <form id="request_details" name="request_details" >
+ <div class="form-row">
+ <div class="msg_list">
+ <h4 class="msg_head"><u>Request Information</u></h4>
+ <div class="msg_body">
+ %for index, rd in enumerate(request_details):
+ <div class="form-row">
+ <label>${rd['label']}</label>
+ %if not rd['value']:
+ <i>None</i>
+ %else:
+ %if rd['label'] == 'State':
+ <a href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}">${rd['value']}</a>
+ %else:
+ ${rd['value']}
+ %endif
+ %endif
+ </div>
+ <div style="clear: both"></div>
+ %endfor
+ <div class="form-row">
+ <ul class="manage-table-actions">
+ <li>
+ <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='Edit', id=trans.security.encode_id(request.id))}">
+ <span>Edit request details</span></a>
+ </li>
+ </ul>
+ </div>
+ </div>
+ </div>
+ </div>
+ </form>
<form id="show_request" name="show_request" action="${h.url_for( controller='requests', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
<div class="form-row">
%if current_samples:
1
0
03 Mar '10
details: http://www.bx.psu.edu/hg/galaxy/rev/bb7c2b314e3e
changeset: 3468:bb7c2b314e3e
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Tue Mar 02 16:40:40 2010 -0500
description:
First pass of the new lastz paired reads tool. Tool page help and info needs to be corrected for this version of the tool.
diffstat:
test-data/lastz_paired_input2.fasta | 703 ++++++++++++++++++++++
test-data/lastz_paired_input3.fasta | 2 +
test-data/lastz_paired_input4.qual454 | 700 ++++++++++++++++++++++
test-data/lastz_paired_out1.sam | 2 +
tool_conf.xml.sample | 1 +
tools/sr_mapping/lastz_paired_reads_wrapper.py | 756 ++++++++++++++++++++++++
tools/sr_mapping/lastz_paired_reads_wrapper.xml | 371 +++++++++++
tools/sr_mapping/lastz_wrapper.xml | 4 +-
8 files changed, 2537 insertions(+), 2 deletions(-)
diffs (2583 lines):
diff -r 765c454bcaa7 -r bb7c2b314e3e test-data/lastz_paired_input2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lastz_paired_input2.fasta Tue Mar 02 16:40:40 2010 -0500
@@ -0,0 +1,703 @@
+>F2YP0BU02IPIOC length=313 xy=3454_0058 region=2 run=R_2009_09_24_17_10_49_
+TTTTTCCTCACAAGCATCACCATTCTGACCTTTATTATGATAGATTTATTTTGTCAGTTC
+TTAAATATCCTATAAAGAGAATAATACAGCATGCACTCTTTTTGTCTAGCCTCTGTGCTC
+AGTGTAATGTCTATGGGAGTCATCCACGTTAAGTATGGCAATAGCTCATTCTTTTCCATT
+GCTGCATAGTATTCCATTCTATCAGTCTATCATGTTTTATTTATCCATTTTCCTGCTGCA
+GATCATTTGGGATCATTTCCAGCTTTTGGCAATTATGAAAAATCGTATAACTTCGTATAA
+TGTATGCTATACG
+>F2YP0BU02GASSR length=219 xy=2466_0953 region=2 run=R_2009_09_24_17_10_49_
+TAATGAATAAGCATGAAGACAAGATTAGAGAAGAATGAAGGAATGAACAAGCCTCCAAGA
+ATATGGCACTATGTGAAAGACCAATCTATGTTTGATTGGTATACTTCGAAAGTGATGAGG
+AGAATGGAACCAAGTTGGAAACACTCTTCAGCGTAATAACTTCGTATAGCATACATTATA
+CGAAGTTATACGAATCATTGTTGTCTCTCCTGGTGGCAG
+>F2YP0BU02HLXG3 length=220 xy=3003_0293 region=2 run=R_2009_09_24_17_10_49_
+TTCATTTCCTTTGCTGCTTTCCCTTCATCTCCTCAATCCACAAACCGTAATAACTTCGTA
+TAGCATACATTATACGAAGTTATACGATCCAATTTCCTAACTTCTAAAATGAGAATTAAT
+CCTAATGCACTGCTCACTTCCCAGCAAGGGACATTCACTTTTCCACAAGAGCTCTCTTTA
+CAAAGCAATTCAACAGCTAAGGCAATGAAGTCAGTCAGTA
+>F2YP0BU02GF6D7 length=134 xy=2527_1997 region=2 run=R_2009_09_24_17_10_49_
+GAGAAGCATCAAATTCAACTCCATATCTGAAGTCAAGCCGTAATAACTTCGTATAGCATA
+CATTATACGAAGTTATACGAGAATTTGTGGTTCCTAGTTCTCAGTGTAATACTCCTTCCA
+ATATATATGATAGG
+>F2YP0BU02G6NFT length=92 xy=2829_0151 region=2 run=R_2009_09_24_17_10_49_
+TCTTCTCTCTGCCATTCTGCCAGGCTCAGTCGTATAACTTCGTATAATGTATGCTATACG
+AAGTTATTACGTATATATATGTGTGTATATAT
+>F2YP0BU02GD65M length=129 xy=2504_3880 region=2 run=R_2009_09_24_17_10_49_
+TTTAATTGGTTGTCTGGCTTTCTTATTGATGTGTCGTAATAACTTCGTATAGCATACATT
+ATACGAAGTTATACGAACAAAACAATAAAGAGATTATAATGGAGCTGAAAATTACCTATT
+GCCTAGTGA
+>F2YP0BU02GW28F length=318 xy=2720_0525 region=2 run=R_2009_09_24_17_10_49_
+GGTTTGAGCCACTGTGCCTGGCCAATTTTCTATTTTGTAGAGACAGGGTCTCACCATGTT
+GCCCAGGTTACGTAATAACTTCGTATAGCATACATTATAAGAAGTTATACGACATGTCTG
+CCGAAAGCTCAGTGGCAGGGCGGAGAGGGCCTGGGGCTGCCTCGTGAGGTGCGAGGGGTT
+CTTGTGAAGGTGGGGAGGCCCAGGGTCAGGGCCTCCCAAGGTAATGCTGAAGGGGCTCTG
+CTTCCAGAAGGGCCTGGACAACCTCAGAGGTCAGGGTGTTGAGCCAGGGGGCTCACCTTC
+CTCTCCTGCCAAGGGGCT
+>F2YP0BU02HKJIX length=388 xy=2987_1095 region=2 run=R_2009_09_24_17_10_49_
+TTTTATTGTGACTTTTATAAATGGAGATCATTGGGTAAAACGTAATAACTTCGTATAGCA
+TACATTATACGAAGTTATACGAACAAAGATAAGGAAATGGCAGGAGTGTTGCAGAAAGCA
+GTGGTTTCTGAAGACACAGGTATAGGCAGATATGAAATACAGAGAAGAAATTTGAGCTGG
+CGCTTCCAAATAACTGTACTTCTTTAGTGGTAAGATATCCCAAGCTTTGATTTCTCATCT
+TATTCACTTTGTCAGGAAGAGACAAACAGGTGTGGGTGCTGGGCAGAGGGCTTGATCTCA
+TTTTGCAGAGAAAGTGTTTGGAGACTTTGAACTAAGCAAAGAGTAACAGGGAAAATAAGA
+TAAAAATGAAAAGGGTAATGATTCGGAG
+>F2YP0BU02H80VC length=67 xy=3266_0534 region=2 run=R_2009_09_24_17_10_49_
+CTATGTTGACTAGGCTGGTCTCGAACTCCTGGGCTCAAGCAGGCCTTGTGCCTCGGCCTC
+CACCTAC
+>F2YP0BU02IO6IM length=284 xy=3450_0684 region=2 run=R_2009_09_24_17_10_49_
+TTGAACGGAATCGAATGGAATCATCATGGGATGGAAACGAATGGAATCATCATCGAATGG
+CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGATGAATGGACTCGAATGGA
+ATCAACATCAAACGGAATCAAGCGGAATTATCGAATGGAATTGAAGAGAATCATCGAGTG
+GACTCGAATGGAATCATCTAATGGAATGGAATGGAATAATCTATGGACTCGAATGCAATC
+ATCATCGAATGGAATCGAATGGAATCATCGAATGGACTCGAATG
+>F2YP0BU02GU7ME length=113 xy=2698_3012 region=2 run=R_2009_09_24_17_10_49_
+CCATATCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGAGATATTCCAGTC
+CGTCATTAAAATTAGATAATTTACGCCTAATAATTATATGTATGTATTGAAGC
+>F2YP0BU02HYBDH length=366 xy=3144_0643 region=2 run=R_2009_09_24_17_10_49_
+TTTTGTTATATTCAGGCCCGCAATGTATTGGATCGTATAACTTCGTATAATGTATGCTAT
+ACGAAGTTATTACGTTTAATTCGATGTTGTCCATGAGTTTTGTTTTTCTATTTAGTTGCT
+ATGTTTGTTTTAATGTAAGGCAAGATTAAAATATTACACTGTCACCGTTACTACCATCCT
+CCCCAAATCCCCCTGTATTAGCTACCTAGGCTTGCTGGGTAACAAATTGTCACAAATTTA
+TTAGCAAAAGAACACACACTTGCTATATCACTGCTCTGTAAGTCAGAAGCCCAGGTGGGC
+TCGACTGGGTTCTGCACTTAAGGTCTCACAAGATTGAAATCAAGACATCAGCTGAGCTGG
+GCTCTT
+>F2YP0BU02GS94E length=98 xy=2676_3052 region=2 run=R_2009_09_24_17_10_49_
+AGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGCAGGCACTGAGGAATG
+GTGAGAGGCACTGGGAATGGTGAGGGCGACTGGGAAGT
+>F2YP0BU02GFM2N length=339 xy=2521_1533 region=2 run=R_2009_09_24_17_10_49_
+GGTTTAATTGCTCATTCAGTAGGTAGTAAACTGCAATTCAATCAAGCATGCTAAACCATT
+GAAAATGAATGCATTACCAAGTATGAATAACTTGTTCATAATTCATTGAGCCGGCCATAG
+GGCAGGCACAACTAAGAGGCATTTGGCAACCAAAGCAATGCAAGCTGGTTGTGAGGAGAA
+AGAAGCTAGGATGCCTAAGAACAGATAGAAGAGCCTACCAGCCACTGACTCAGGTACAGA
+GCTAGTCACTAAAGATGAATATTGGTCTGATGACTACCGTCCGTAATAACTTCGTATAGC
+ATACATTATACGAAGTTATACGAGACATGAACAGAAATG
+>F2YP0BU02H2R5T length=71 xy=3195_0127 region=2 run=R_2009_09_24_17_10_49_
+GCAGCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGAGCCTCATTCTCTTT
+AAATGTAGACA
+>F2YP0BU02IENAS length=319 xy=3330_0738 region=2 run=R_2009_09_24_17_10_49_
+TTTGTATAAAGTGAGAGATAAGAATCCAGTCGTAATAACTTCGTATAGCATACATTATAC
+GAGGTTATACGATATTCTGTATAGAGGTGATGGCTCATATAATTCAGCTGTGATAGCCAT
+AATTTCCAAAATGACAGTAGGAAAATAATGTCTCATGGAGATAAAGGAAACTGACAATAA
+AAATGGAAGAAGTACAAAAACTGCCATGTAAAATAATTCCTGGAAAATTTTTGAAAGTTT
+TGCTGGAAAACTTTTTTGAAAGTTTTGCTGGAAAAGACTACATACTTCTCCAAAAGAAAA
+GTAAACTTCTAAGTGTTAT
+>F2YP0BU02HT2D7 length=41 xy=3095_3085 region=2 run=R_2009_09_24_17_10_49_
+ATGGAGGAGTTGGGAGGACACTGTCTTGTAAGTCTGCAAGT
+>F2YP0BU02H8REW length=269 xy=3263_0566 region=2 run=R_2009_09_24_17_10_49_
+TTGACCCTTGACCTTTAGCTTCCTTCTTCCTTAACCAGCAAACCTCCATGCCCTATGTCT
+CCTAAATGTCCTTCAAATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGA
+GAAAAGGTCTTTGTTACTCATGGCACAGAAAGAAGCATGAGCTTCATGTTTGCATCAGTT
+CTTCTTGCTCTCCAAATCCCAAAGTAGGCAAGGTGGAGGTAGGCCAAGGTAAATTCTGTG
+AATCCAGTGAGTTTATGACACAGCTGAGG
+>F2YP0BU02IAR6Y length=369 xy=3286_0680 region=2 run=R_2009_09_24_17_10_49_
+TTTTGCTGAGAAGCAAATGCCACACAATCAATAACTCGTAATAACTTCGTATAGCATACA
+TTATACGAAGTTATACGATGAGAAAGGGAAAATGGCTCCTGAGAGTCCACCCTTGTGGAC
+TGCTATACTTGTCTGGTAGGAAAATTAATTTCAGTTTCTATGAAGGCATTGAAGTTGTCA
+ATATTTATTTCAATATTATTAATAATAATGATGTTCCGACATCCTGAATTCCAAGTTTCC
+TGCCACTTAAACCAACTGGAAAACCACTGTTTTAGATGGCTTTTCTAAAAGCCCACCCCC
+ATCAACAAGATACCCAAGATAGAGGGACTTACATGAAACATTCACTGAATGCTCCCAGAT
+GGGTACAAG
+>F2YP0BU02I3TZY length=65 xy=3617_0268 region=2 run=R_2009_09_24_17_10_49_
+TGGAATGGAACGGAATGGAATGGAATGGAATCAACCCGAGTGCAGGGGAATGGAATGGAA
+TGGAA
+>F2YP0BU02JP6S8 length=265 xy=3871_2922 region=2 run=R_2009_09_24_17_10_49_
+TTTGATCCCTTTTCCCGCCATCTTCTATGGCAACTCTGGCATTTACACCTCACTTTATGT
+ACGCCATGGCTTTTTCCATACTTCGAGGAGCCATCGCAGTAATGAGTTCGTGTCATTTCC
+TGTGGTTTTCTCCAGGGTATTAAATCCTGTATTCTGGGAAAGCACTTTCAAATTGATTAA
+TTCTCCCATATTCAAGTTTATATTCCGTAATAACTTCGTATAGCATACATTATACGAAGT
+TATACGAAGTCATTGTGTGAACATT
+>F2YP0BU02IG2DL length=165 xy=3357_2999 region=2 run=R_2009_09_24_17_10_49_
+TTGTCATAATTTGTTACAGTAGTCACAGTAAGGTTATTCAATACTGTAATTACATTTAGA
+ATCAATAATAGTAATATATCCACAAACCACAAATATTGAAATTAATATGCCTCTAAATAT
+CGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGCCTA
+>F2YP0BU02I6OA8 length=121 xy=3649_1794 region=2 run=R_2009_09_24_17_10_49_
+TTGCAGATTGCACTGAGGATTAGAGACAACATAGAAGCGTAATAACTTCGTATAGCATAC
+ATTATACGAAGTTATACGATTGAGAGATGCCTGGGTGAATCACAGACGTGAGTGGTGGAC
+A
+>F2YP0BU02JHJNK length=351 xy=3773_1070 region=2 run=R_2009_09_24_17_10_49_
+TTTTTAAACCTGGAAAATACACCAAATTTCAATTAAAAATGAAAATGGAAAGATCAAACA
+AGACATAAATAGAATCAGAAAGAATAGGGTTCGTATAACTTCGTATAATGTATGCTATAC
+GAAGTTATTACGAGTAGAGTCTTTTATAAAAACATCGCAAGATGTGCGAGGAACTAAAAC
+ATACTAAGGGGGAAGGATTTTTAACTCGGCCCCAGCAAAAAGAACTCTGTGCCCCTCCAT
+GGCCCTGGATGGCGGATGAGAGAGGGGCTCGCCTGCTCACAGAGCCCTAAGGACGGCGCC
+TCCGTGGCTCGAGCTTGTCTAAAGGGACTTGGAAGGTGTCTGGTGAAAAGG
+>F2YP0BU02JWZQ1 length=307 xy=3949_0875 region=2 run=R_2009_09_24_17_10_49_
+GGTTGTGCTTGAATTGGACAGATCCAGTGAAACTAATCAAGTACCTACTATGTGCCAAGC
+ATTGTGTCAGATGCTCTCACATGCATTATCTTGGAATCGTATAACTTCGTATAATGTATG
+CTATACGAAGTTATTACGCAAGCGTGTATTAATGGTACTAATTTCTGTAGTGCTATGAAT
+AGAATCTTACTATTTTGTGTCTAGTCTTTTTGTTCAACATTTGCGTGTGAGATTCATCCA
+TGCTGTTGAACAAAGTTCCATGTCATTCATTTCCATCATTTTATAGTACATTGGGTGATT
+AAACCAC
+>F2YP0BU02G4WWP length=149 xy=2809_1031 region=2 run=R_2009_09_24_17_10_49_
+ATTAAGTGAATAGTGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGATA
+ATATCTACCATATTGAGCTATTTTAAGCAGTAAATGAATAAAATACGCAAAGTGCATAGC
+ACATGGTAGATAATAAAGGAAGCTATTTC
+>F2YP0BU02IDILN length=130 xy=3317_1241 region=2 run=R_2009_09_24_17_10_49_
+TTACATAGTTATAGTAATCAAACATTATGATGCTCACATAAAACAGATACATAGATCAAT
+GGAATATAATAGAATACCCAGAAATAAGCCTATGCATATACAGTCAACTAATTCTTGAAC
+AAGGCACACA
+>F2YP0BU02I80Y8 length=435 xy=3676_0930 region=2 run=R_2009_09_24_17_10_49_
+TTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGGTCTCAA
+GTGATCCACCCACCTCGGACTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCTACTTC
+TTTCTTTAACCTTCAGCTCATGGATCCCCTACCCAGCAAGACTTCAGGGCCCTGATGGGT
+TAGATGCCCCACCTCTGCTCTTCCATAGTGTTCGTAATAACTTCGTATAGCATACATTAT
+ACGAAGTTATACGATAGAAAAGTGTGCCACCAAGAAAGACCTGCATTGGAAGGGCTAGAT
+GTGTGCTGCATATGCTGCATAGACCTTTACAGGGGAGTCTCTTTTCTCCTTCTTGCTTCC
+TTTGCACAGAATCACCATAGGATATCACAGGAGCTTGTGCAGTTGGACTGAGACCGCCAA
+GGCACACAGGGGATA
+>F2YP0BU02JWZ8I length=437 xy=3949_1504 region=2 run=R_2009_09_24_17_10_49_
+TTTTTGTCAAATAATAATTCTATTACCAGCTAAACTATCAATCATCGTATAACTTCGTAT
+AATGTATGCTATACGAAGTTATTACGTGCTAAAACATTCAGCACGCTCCTCCTCTCTGCA
+GCCCATAGCCCAGGTACCTTAGTGCAGGGTGGAGGAAGCCTTGGGCAACCTGCTCTGTGA
+TGAGCAACCTATTCTCCTAACAGCCCGAGCCTTCCACCGCCCTGAGGCCTTGAAGCACCT
+TGGGGATGGCCTTCCTGCCTCTGCCTGGGCCCTCGCTGCTTCTGTCTGGAACTTCTCCTC
+CCAGTCCACGAGAGATAGCTTGAATCTTGTCCTGAAGACAGGGCTACAATGTTGTTTCGT
+TTTTACATCTTTCCCTGAATATTCTTTCCTGAATGTATGGCTTCTTTGTCTCTGTGTCTT
+GTCACCTTATGTTGTAT
+>F2YP0BU02J14RD length=322 xy=4007_3079 region=2 run=R_2009_09_24_17_10_49_
+AATTTGGAATATATACACCATGGAATACTACACAGCCATAAAGAAATGAGATCATGACAT
+TTGTAGCAATGTGGATGTAACTAGAGTCCATTATCCTAAGCAAACTAACACTGGAACAGA
+ATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGAAAATCAATTCCTCCTT
+TCTATTTGTGGGCCAAATGATTTCATTTAAGTCACTTAATTCTGACACTCAGTTTCCTGT
+AAACTGTAAACTCTAAAATGCAGATTACAATACTCATCTTGTCTACCCAGGTTATTGTGA
+AAATCAATGAATTAATATACGT
+>F2YP0BU02GCKL1 length=376 xy=2486_1735 region=2 run=R_2009_09_24_17_10_49_
+GTTTAAGTTCAGGTTCACATAAGAAATGGGTTTGAGTCTTCCACTGACCATATCATTAAG
+GAATGCAACAGCCATCTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGGT
+ATTTCTTATTGTCATCTTCAATACTTAGTATCTATAAATTATAAACACTTTTGGATTTTT
+GTGGGTTTTTTCTCTCAACTGGAAAGCAAATACAAATAATAACATCTTTAAACAGAATTA
+ATCTTTAGATGTAGTAGAAGAGAATGAAACAATTGGGTTTTGGGGTTTTTTTGTTTGTTT
+GTTTGTTTGTTTTGCTTTTTGTAAACAGAGTCTTACTCTGTCGCTCAGGCTGGAGTACAG
+TGGCTTGATCTCAGCT
+>F2YP0BU02HV3CE length=220 xy=3118_3420 region=2 run=R_2009_09_24_17_10_49_
+AACCAGAATGGTGGTTCATCAGGAAATTACAACAATTAACATAAGTGCTGCAAATCGTAT
+AACTTCGTATAATGTATGCTATACGAAGTTATTACGAGACTACATATGATATTACTTAGA
+AAAGACGCTGTGGAAGTCTAACTCACATTTAAATATACTAAGATTATTTCATTCTAAAAT
+AATGAAACCATTCAGTTCTTTATCTTAGAAGGACATGATA
+>F2YP0BU02J45XB length=51 xy=4042_1197 region=2 run=R_2009_09_24_17_10_49_
+CAAGGACTAATGTCCAGAATCTACAAGGAACTCAACAATCAGCAAGAACAA
+>F2YP0BU02FXSE6 length=214 xy=2318_0144 region=2 run=R_2009_09_24_17_10_49_
+GTTTTCACATTGTTGGTGGGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTA
+CGAGACTGACACCTGGAGAAGTCCAGCCCTCTTGAAGGAAGGCAAACCTAAATCTTTTAA
+AATAGAAAAGCATCTTATTTTTAAAGGCTTCCAGAGACATCAAGTTCACAATTTTCCCCT
+AACTTACTGTTGGGAAACCTGTTAAAAATATACT
+>F2YP0BU02GA5V8 length=62 xy=2470_1542 region=2 run=R_2009_09_24_17_10_49_
+TCCATTTGAAGAATGATTTCCATTCGAGACCATTCGATGATTGCAGTCTGTCATTGACTA
+GG
+>F2YP0BU02HKT8Z length=297 xy=2990_2705 region=2 run=R_2009_09_24_17_10_49_
+TTTACTAATATTATCTCATTTAATACTCTCAACAAGCACACAATGTACGTATTTATTCTT
+TCATTTAATAAGTATTTATGAAATGCCCACTACTATTCACCCATGATATTCGTAATAACT
+TCGTATAGCATACATTATACGAAGTTATACGATTTTTCAAAAACAAAAGTCACATTTAGC
+AAAATATTCAGTACTGGTGATCTGGGTAAAGGGTACACGGGAATTCTTTGCACTATTCTT
+GCAATATTTCTGTAAGTTTGAAATTCATTCAGAATAAAAGAAAAAGATACTAGTGTT
+>F2YP0BU02G42KJ length=363 xy=2811_0177 region=2 run=R_2009_09_24_17_10_49_
+GTTTCCTTCTCCACACCAGCCCCTCTACACATCACAGGTGACTCTAAGCGTAATAACTTC
+GTATAGCATACATTATACGAAGTTATACGAGTCAAGAATGACTGTCAGCTTTGCATCTGG
+AGGAGCTGAGGGGATGATGGTGTCCTTGGCCGAGATGGCACAGCTTGGGGAGGGAACTTG
+TTTGAGGAAGAAAATCAAGAATTCTATTTCGGACAGGCTAAATTTGAGCTTCCTCCTGTA
+CATCCATGTGGGGATAATGAGTAGGCAGTTGGGTATGGGTGGCGGGGGGCGGGGGACGGG
+GAGTGAAGGGTTCGATTTGGAATTATGTGGCAATTAAAACCTCAAAGCTGGCTAAGATCA
+CCT
+>F2YP0BU02HD86B length=333 xy=2915_2657 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTTGTACTTTCAGTAGAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCGATCT
+CCTGACCTCGTGATTCACCTGTCTTGGCCTTCCAAAGTGCTGGGATTACAGGCATGAGCC
+GCTGCACCCTGCTGAGATTTTTATTTTTAAGAAATTATTTAAATGTTATGGTTGTGAATT
+GAGTTATCCCATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGGCTAAGA
+ACTGTATTTGGGAGACTAGTGTTTATATTTGTAGGTAAGGAGGCACACTGGCTTTTGGAG
+TTGTGAGTTGTTGTGCTGATTCTTTCTCACGTG
+>F2YP0BU02F3YKL length=277 xy=2388_1331 region=2 run=R_2009_09_24_17_10_49_
+TTGGGCACTTGTCTCTTAGACACTTTCAAGTTACCTACTGGACAGGAGAGACCTCTTCTC
+TATAAAGTATCACACTTGGAGGCTTTTCAGGCACAGGACCATAGATTGTAATATTTTCCA
+TAGCAGTTGCCCAATTTTATCTGCGTAATAACTTCGTATAGCATACATTATACGAAGTTA
+TACGACCTCACATAGTGCAGTTTGGGTTGAGCGGAGGTGGCCAGTAATGGGGGCCCCTGG
+GACTCCTGGGACCTCTGTCTTCTTCTCCCTGGAAGAG
+>F2YP0BU02HLAR5 length=447 xy=2995_3651 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTGGTATTTTTAGTAGAGACGGGGTTTCACGGTGTTAGCCAAAATGGTCTCGATCT
+CCTGAGCTCATGATCCGCCCGCCCCAGCCTCCCAAAGTTCTGGGATTACAGGCGTGAGCC
+TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGCCCCCTACTGGTCTGTGG
+TTGTTTTTCTGTTGGCTGCAGCAGGCTGGCTGTGGTTTTTCNCTTGCCATGACAACTTCT
+AATTGCCATGTACAGTATGTTCAAAGTCAGGTAACTCCTTATTGTAAGCAAACTATGTAA
+CTGCCCAGAGCAGCACATATAAACCAGCCTAATGTGAAAAAAGAAGAAATAGGCCGGGCG
+CAGTAGTTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGGATCACGAAGC
+CAGGAAATCGAGACCATCCTGGCTAAC
+>F2YP0BU02GGSTZ length=300 xy=2534_2405 region=2 run=R_2009_09_24_17_10_49_
+TGGATGGACTCATCATCGAATGGATTCGAATGGAATCATCGAATAAATTGATTGAAATCA
+TCATCGAATGGAATCGATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGC
+GAATGCAATCATCATCGTATAGAATCGAATGGAATCATCGAATGGACTCGAATGGATTAA
+TCATTGAACGGAATCAAATGGAATCATCATCTAATGGAAACGAATGGAATCATCATCGAA
+TGGAAATGAAAAGAGTCATCATCTAATGGAATTGCATGGAATCATCATATAATGGAATCG
+>F2YP0BU02JARMH length=257 xy=3696_0199 region=2 run=R_2009_09_24_17_10_49_
+TTACATTTTGCTCTCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGATTCT
+GGGATTATAGGCCTGAGCCACTCAGTCTGGCCAATAATAACAAATTTAATTATTTTAAAA
+GTATTACTGTATTTCAGTCTTCTTTCAGCCTACAATATGGTATTAAATGCCTTACATGGA
+GACATATAAAGGATTTTACCATAATAACCTTTAAAACAAAAGTGATTTCCTAGAATTATA
+GGACAGAAAAAGAATGT
+>F2YP0BU02F6FA3 length=174 xy=2416_1645 region=2 run=R_2009_09_24_17_10_49_
+TGTTTCTTTAATTCTTTGAAGGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTAT
+TACGCTTCCACCAGTGTGCATGCTCAGATTTGAAGTGAGTGTACACTGTGCCCAGAGGCT
+GTCTATGATGCCCCAGTTGGTCTTTGCATTTACTCCAGGCACGCCTTGCACACC
+>F2YP0BU02IE523 length=281 xy=3336_0509 region=2 run=R_2009_09_24_17_10_49_
+TTCTTTCTTTCTTTCTTTGTAGAGATGAGGTCTCACTATGTTGCTCAGGCTGGTTTCAAA
+CTCCTGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGAAAATCATTCTA
+CAGCACAGGTCCTCCCAGGTCCATGACTTACTGAGTAGATAAATGTAGCCAATACATGAG
+AAATCAAGTTAAAACCTGTCCCTGCTGAGCCAGCAGTATCTATAGCTGGGGTACTACATA
+AGTGGATTCTGGGGAGCTTATTTAGAAAAAGACCCATGGCT
+>F2YP0BU02HZ814 length=271 xy=3166_0842 region=2 run=R_2009_09_24_17_10_49_
+TTTATAATAAAATGCAATTCCTTAAAATAATTCAATCGTATAACTTCGTATAATGTATGC
+TATACGAAGTTATTACGTGACAAATCACCAGTCGAGAACTGAGCACCTTGAAATTGTGAC
+CAAATGGAATACAAAAGGTTTTTATGGACGGCTCAAAGGTTTTCATGGTTATGCAAACCA
+CTGAAAATTAGCTAGTTCAAATATATTTGATGGTACAGAAAAATATTCCCTTCACCTAGC
+AAAATGAATATAACAAAATATGGCAATCTGG
+>F2YP0BU02F8YG5 length=285 xy=2445_1015 region=2 run=R_2009_09_24_17_10_49_
+TTGCATTACCCAGAATTGGCCACCAGGGTAGGCTAGAGTTCGTATAACTTCGTATAATGT
+ATGCTATACGAAGTTATTACGCTCTTTGTTGATCCTAAAAGAAAATGGCAAGAATTTAAA
+GTGGTTTTGGATTGACAGTACCACCAAGAACCCAGCAGAAGCAATGCAGATCCTTTCTGG
+ATGAACTCATCTTTAATCTAGGCCTCGGGGAATTTCCACAGATACAGTTCCAAGAAAATA
+AATTGTGGTCAAAAATTCCAAACAAATAAGGAACGAGGCACCAAG
+>F2YP0BU02GJK8J length=290 xy=2566_1457 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTCTTCTTAATAACTGAAGAGAATAACATTTATCAAACAAACGATCGAACTCTTTC
+TGAGACATAGTTTCATGTGCCTCTTTGGAGTTGATTTCCCCTCCGTAATAACTTCGTATA
+GCATACATTATACGAAGTTATACGAGTGGCCATCAGGACATTTATTAGCTGTTAATCTAA
+CCACTACCAAATGCATTAACACATTTTTTTTGACAACTTTTTCTCTTTTATTTGGCTGTT
+GCTTAGTTCAGTTTTGCTTGGAGAAGTTGTGGCAATCCTGAATTCAGTTT
+>F2YP0BU02IFF38 length=137 xy=3339_1222 region=2 run=R_2009_09_24_17_10_49_
+TTGAGAATCAAATTTCACCATTAGTTTCTGAGGGAATCGTATAACTTCGTATAATGTATG
+CTATACGAAGTTATTACGGTCAAAATAAAAAGAAAATATAGGAAGAACAGGTAAAGAATG
+GTGAAAAATATCATTGT
+>F2YP0BU02JGYZX length=265 xy=3766_2971 region=2 run=R_2009_09_24_17_10_49_
+ATTTGAGTCCATTTGATGATTGTTCCATTCGATTCTATTCGGTGATTCCATTCGATTCCA
+TTTGATAATGATTCCAATCGAGACCATTCGATGATTCCATTCAATTCCATTCAATAATGA
+TCCCTTTCGTAGTCCATTCAATGATTCCTTTCCAGTCCATTCGATGATTCCATCTGATTC
+CATTCAATGAATCCCATTCGATTCGTAATAACTTCGTATAGCATACATTATACGAAGTTA
+TACGACATTCGATTCCATTTGTATG
+>F2YP0BU02JT6YF length=104 xy=3917_1317 region=2 run=R_2009_09_24_17_10_49_
+TTCCTAGGGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGGACCTGCTC
+AATTTAGATTCCACTTCCAGGAGTATGAGGATCTTCTCCTGGGA
+>F2YP0BU02FL7V0 length=282 xy=2186_0990 region=2 run=R_2009_09_24_17_10_49_
+TTCCCCAAACAGACCCTAGAATAGTCTTCCTTGGAAATTCCATGAGCAAATAGCGTAATA
+ACTTCGTATAGCATACATTATACGAAGTTATACGAGTCTGTTTTAGATAAATGATGTTCA
+GTGGACCTTTCTGTGATGGTGGAAATATTCTATATTTGTGCCATTCAATACAGTAGCCAC
+TAGACTATTGGTCTATTTGCACTTGAAATGTGGCTAATGAGACTCACAAATACAATTTTA
+AATTAATTTAATTTAACTTTAAATAACAACACGTATTTTATT
+>F2YP0BU02JF57F length=249 xy=3757_2521 region=2 run=R_2009_09_24_17_10_49_
+CTATCTACAAGTGAATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGTAA
+CTTAAGAAAACACTCCACCATTAGACAAACAAAGGCACCAGAATGCAATGAACTATAATA
+CTTTACCCATTAGGTGAGTAAGAGCCAGTAAATCAAAGGGCTTTTAAAAACACAATTCCT
+CAGCTAACACCATGAAGCAAAATTAACCATATTAGTTCTCTTCAATTTTACACTTTTGGG
+GTTAGGTAC
+>F2YP0BU02IADK7 length=500 xy=3281_2233 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTTGAGATGGAGTCTCACTCCGTAGCCCAAGCTGGAGCGCAGTGGCATGATCTTGG
+CTCACTGCAACTTTGCCTCTTGGGCTCAAGTGATTCTCCTGCCTCAGCATCCCAAGTAGC
+TGGGACTACAGGAATGCACCACCACACCCAGTTAATTTTTTTGTATTTTTACTAGAGACG
+GGGTTCCACCATGTTGCCCTGGGTGGTCTTGAACTCTTGAGCTCAGACGATCCACCTGCC
+TTGGCCTCCTAAAATGCTGGGATTACAGGCATGAGCCACCATGCCCAGCCATTAAGTGGT
+ATTTCTACGTTTGCATGGCATGTGACTAAATTGATCAATATTCAATATCATGAAGGTGTG
+TGTTTGCATAATGTTGACCGGATCTAATAGGCAAACAAAGGGATATGTGAACAGAGTTCA
+AATGTATTTTAAAGATATTACCGTAATAACTTCGTATAGCATACATTATACGAAGTTATA
+CGAGCCACATTATTATTCTA
+>F2YP0BU02H62VV length=305 xy=3243_4041 region=2 run=R_2009_09_24_17_10_49_
+CTTAGATCACAACACCTAAGTCCTTTTGAATAACTGGAAGCCTTCGCAAGAAGGACAGGT
+ACAAAGAAGCTCAGACTGTAAGAACTACAGTAAATACCGAACTCTTCAAATCCCAGGAAC
+AGATAAACATCCACAAGCATCAAGACCATCTAGGAAAACATGACCTCATTAAATGAACTA
+AATATGGCACCAGGGACCAAACCTGGAGAAACAGAGATATGTGACCTTTCAGACCGTAAT
+AACTTCGTATAGCATACATTATACGAAGTTATACGAGAACATCATGGGTCTTCTAAGTAT
+GTCAC
+>F2YP0BU02GQK0T length=370 xy=2646_0091 region=2 run=R_2009_09_24_17_10_49_
+AGTGTTCTCCTTCATGAATGAATGGTTCCATCTATGTCTGCTCTATCTCAGTCGCCAGAA
+TAATGAATCAAAGAATAATTAAGCCTATTAATAAAATGGTCAATTTATTTTAATTTATTG
+GCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGAGGCACAGAAAGACAAAT
+ATTGCATGTTCTGACTCTTGTGTAGGAACTAAAAGGTTGAATTCATTGAGATAGAGTAGA
+ATGATAGATACCAGAGGCTGGGAAAGGTATGTGGGTGGGCAAAATGAAGAGAGGTAGGTT
+AATAGGCACAAACAGGAAGTTATTTGGAAGGAGCAAGTTCTAATGGTTGATAGCAGAGTG
+GGTGATTAAG
+>F2YP0BU02JPJK8 length=198 xy=3864_1498 region=2 run=R_2009_09_24_17_10_49_
+CACAGTACCATGTCACACTGGCATTGCCTGAATCATTGCCTGAATTCAGCATAGCCTCTG
+CGCACCAGGTACTGTTCCAGGTGTCAGGGATATTGTGGTGAACAGGACAGACAAGGTCCA
+GGCCTCGTGGGGTTACGATTCTGGTGGGAGCGTATAACTTCGTATAGCATACATTATACG
+TAAGTTATACGATCTTTA
+>F2YP0BU02JYTJJ length=335 xy=3970_0125 region=2 run=R_2009_09_24_17_10_49_
+GTTTATCTTTCTTCTCATTCCATTTAAGGTCAATCTTTCCTCTAGTGCTCTTCATCCTAT
+CCCCACTTCCCTTCTTATCTAAACTCTTGTCTAGGAAATCTCATTAGCTCCTTTGGCTTT
+AACTACTAACTGATTACCTTCAGCTCAGTACTCCTGAGGAATATATCCCCACTCGTATAA
+CTTCGTATAATGTATGCTATACGAAGTTATTACGTAAAACAGCTAGGTGTTTCTGCTAAG
+AAACACTGCGTGGTAACGTTTCCCGGATAGCCCCAAAATGATCTCTATCTTCTGGTGTTT
+ACACCATGTGTAGTCCCTTCTCACAATATACATAC
+>F2YP0BU02GWFAR length=384 xy=2712_2273 region=2 run=R_2009_09_24_17_10_49_
+TTCTAAGATAGAAGTTTAGATAATTAATTTTGTAACTTTATTCTTTTAAATACATGCACT
+AAATGTTACAAATTTCCCTCTACACACTGCTTTTGCTGCAGACTACAAATTTTAATTAAT
+ATATTTTTATTTTATTGATTATTATTATTATTTAACGACAGGGTCTTGCTCTGTCACCAG
+GCTGGAAGGCAAGTAATACAATCATAGCTCGTATAACTTCGTATAATGTATGCTATACGA
+AGTTATTACGAATCCTTTGGGTATGTACCCGTGATGGGATGGCTGGAACAAATGGTTATT
+TCTAGTTCTAGACCCTTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTA
+CAGTCCCACCAACAGTGGAAAAGT
+>F2YP0BU02JXVRY length=55 xy=3959_1420 region=2 run=R_2009_09_24_17_10_49_
+TTACCCTTCTGTATAATGGAGATGGCTTATTTTCTCAAACCTCATGAACTACCCC
+>F2YP0BU02JWAD0 length=227 xy=3941_0774 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTTTTTAACCAAAGGACTAAAGTCATAGGAAGAAAAGCATACACTGGTTTTCTGGA
+CATTCCCCTGGGATTATACACACACACCATGCAACAATCACAGGCACCAGCTCCCAGCAG
+GCACATTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGTGCAGCCCAGCC
+AGGGGCGGAGGAAGGCAGGAGTGGGGTCTGCAGCTGTCACCCGGAGC
+>F2YP0BU02GX9F0 length=48 xy=2733_1982 region=2 run=R_2009_09_24_17_10_49_
+AGTTCCGTGAGGACAGGACTATACAGTCAGCCCTCAGTATCCATGGGG
+>F2YP0BU02GRICP length=451 xy=2656_2327 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTTTTTTTTTTGGTAGAGACAGGGTTTTGCTGTGTTGCCCAGGCTGGTCTCAAACT
+CCTAAACTTAAGTGATCCGCCCACCTCAGCCTCCCAAAGTGCTGGGATTATAGGTGAGAG
+CCACTGCGCCCAGCTCACGATTGTTAAATCTAAGGGCTCTGAAAATAGCAAGTTTTTGTA
+TAATTGTTTCAATGGCAAGACCTGGCCTGGACTGATGTGAAGCCGCTGGTTGTTGTTATT
+CCATCACTTCAGCTGCAGAAATACTGTGTTTATTGTGGGGGCTGCCCAGACCTGTGGGTG
+GCACTAGATAATCGACAGGAGCTCCCCTTGTAGCGTAATAACTTCGTATAGCATACATTA
+TACGAAGTTATACGATATGTGTACCTACTATTTTGGGACACAAGGGTATTAAAAACCATG
+TACTCAAGGGCTGATATTTAATAAAATTAAT
+>F2YP0BU02GIUVR length=132 xy=2558_0069 region=2 run=R_2009_09_24_17_10_49_
+ATTAGGCTGATACTACCTGAATCCAGCTTAAGACATAAAGTCATTATGTCGTAATAACTT
+CGTATAGCATACATTATACGAAGTTATACGATTGAAGGTCACCAAACCAAATCATAACAA
+TCTTCCTCAAAT
+>F2YP0BU02FJD9A length=189 xy=2154_0348 region=2 run=R_2009_09_24_17_10_49_
+AAAAGAACATGAGTTTCCAGAGCCTGGTGGCCTGGGTTAGAATCCTAGCTCTGCAACTCA
+TGGCTGTGTACTATTTGGCCAAGTAACTTAACCTTTCTGTGCTTTAGTTTCCTCATCTCT
+AAAATATGTATCTTTTTNTTTTCCCTTTCGAGACAAGAGTCTCACTGTGTCACCTCGTAT
+AACTTACGT
+>F2YP0BU02IIGW9 length=372 xy=3373_2971 region=2 run=R_2009_09_24_17_10_49_
+TTTTGTTATATTCAGGCCCGCAATGTATTGGATCGTATAACTTCGTATAATGTATGCTAT
+ACGAAGTTATTACGTTTAATTCGATGTTGTCCATGAGTTTTGTTTTTCTATTTAGTTGCT
+ATGTTTGTTTTAATTGTAAGGCAAGATTAAAATATTACACTGTCACCGTTACTACCATCC
+TCCCCAAATCCCCTCGTATTAGCTACCTAGGCTTGCTGGGTAACAAATTGTCACAAATTT
+ATTAGCAAAAGAACACACACTTGCTATATCACTGCTCTGTAAGTCAGAAGGCCAGGTGGG
+GCTCGACTGGGTTCTGCACTTAAGGTCTCACAAGATTGAAATCAAGACATCAGCTGAGCT
+GGGCTCTTATCT
+>F2YP0BU02JF0IJ length=54 xy=3755_3337 region=2 run=R_2009_09_24_17_10_49_
+AATAATAATATCATGTCCACAGTGGAGGTCTACAGGAACAAAGGAAAGAATAAA
+>F2YP0BU02HU4M2 length=275 xy=3107_3500 region=2 run=R_2009_09_24_17_10_49_
+TGCCTGTAAATAGGAATAATTCTAATAGTAACTCTCGTATAACTTCGTATAATGTATGCT
+ATACGAAGTTATTACGAGCACATAAAGATGAGGATTTAATTTTAGTATTAATGATCTCAA
+AGCTGGTTAATGTCTGACAATGAGCAGATACATGATGCAGGTATACTTCATGAATTTGTC
+TCATTTCTTGTTAGAAGCTGCTAGACTCAGTGAGCTTTAATTTGCTGAGACTGACAAAAT
+AGCAGATTTTCACTGAACCTGACTAGCTGGTTTTC
+>F2YP0BU02H8Z84 length=68 xy=3265_3830 region=2 run=R_2009_09_24_17_10_49_
+TTATTTGTTGCATTTATATGTGGGTAGATCAATAACTTAATTTCTATAGAACAATATTCT
+TTTGTTTG
+>F2YP0BU02F2LFK length=373 xy=2372_3182 region=2 run=R_2009_09_24_17_10_49_
+TTTCCTTTTCACCATAGGCCTGAAGCGATCCAAATGTCCACATCCAGATACTACAAAAGA
+GTGTTTCAAACCTGCTCTATGAAAGGGAATGTTCAACTCTGTGACTTGAATGCAAACATC
+ACAAAGAAGTTTCTGAGAATGCTGCTGTCTGCTTTTTGTATGTAATCCCGTTTCCAACGA
+AATCCTCCCAGCTAGCCAAAATATCCACTTGCAGATTCCGCAAAAAAGAGTGTTTCAAAA
+CTGCTCCTTCAAAACGATGGTTTAGTTCTGTTAGTTGAGTACATACATCTCGTATAACTT
+CGTATAATGTATGCTATACGAAGTTATTACGTATCCACTTGCAGATTCCACGAAAACAGT
+GTTTCAAAAACTG
+>F2YP0BU02HCBFV length=56 xy=2893_2393 region=2 run=R_2009_09_24_17_10_49_
+TTTATGAAACAAAGGAACTTGTCATAGTCTATTAAAGCAATCTCCTAACCCCACTG
+>F2YP0BU02GR0SM length=100 xy=2662_1652 region=2 run=R_2009_09_24_17_10_49_
+TGTTTCTCCATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGTCCAGCAA
+GGTATTTCGATAGGAACTGTGATAATACCAGCCCTCATAG
+>F2YP0BU02GN26J length=416 xy=2617_2441 region=2 run=R_2009_09_24_17_10_49_
+GGTTTATATGTACCATGTTTTATTTATCCCATCCGCTGTTCATGGGCACATAGGTTGATT
+GATTCCATGTCTTTGCTATTTTGAATAGCACTGCAGTGAACATATGGGTGCATGTGTCTT
+TTGGATAAACGAATTATTTTCTTTGGGTATATATCCAGAAGTGGGATTCCTGGTTTAAAA
+TGGTAATTCCATTTTTAAGTTCTTTGAGAAATCTCCAGACTCGTAATAACTTCGTATAGC
+ATACATTATACGAAGTTATACGATTATCTGTATTACAGGGAATAATGTGATATTGGAGTT
+ACTATGTCCATTATGTTTTAAAGCTTTTTCTCAGTTTTAGTACTTTAAGATGACATAAGT
+TGTGTCATCCTTGAATGTGTTGGCTATTGCATGAAAAGACCCTATATTTACTTTTG
+>F2YP0BU02HGJBL length=377 xy=2941_2623 region=2 run=R_2009_09_24_17_10_49_
+TTACAGGCATGAGCCACCGCACCCAGCCTCTATTTCCTTTTAAAATTGAATGCCTTTAAC
+AGCACCCAAGTCACCTCTTGAATGTTGTATTGCTTAGAAATTTCATCCGCCAGATACCCT
+AAATCATCTCTCTGAAGTTCAAATTTCCACAAACCTCCAGGGCAGGGGCAACATGCCACC
+AATCTTTTGCTAAAACAAGTTATAGCAAACAACTTCCTCCGTAATAACTTCGTATAGCAT
+ACATTATACGAAGTTATACGATGATAATGGTAGTTGATAATGGCAGTTCATGGGTGAAGT
+TGCTCAGGAAGAATGAATATACTGTGAGACAAAATGACCACTACTGTTTGAGAGCTACGT
+TGAAGAAGGGGAGCCTG
+>F2YP0BU02HEDVO length=61 xy=2917_0562 region=2 run=R_2009_09_24_17_10_49_
+TAAGCCACTCACACTCCTCCAAAGGCAGTCAGAGCTCCTTCAGCTTGCCCACCTACTCTC
+T
+>F2YP0BU02II7P9 length=196 xy=3382_0847 region=2 run=R_2009_09_24_17_10_49_
+ACAGTGAGACTCTGTCTCAAAGAAAGAGAAGAGGCCTGGTGCAGAGGCTCACGCCTGTAA
+GCACTTTGGGCGGCCGAGGTAGGCGGACCACTTGAGGTCAGGAGTTCTAGACCAGCCTGG
+GCAACATGGCAAGATCCCATCTCTAATAAAATCGTATAACTTCGTATAATGTATGCTATA
+CGAAGTTATTACGTAA
+>F2YP0BU02IDY8I length=200 xy=3322_2320 region=2 run=R_2009_09_24_17_10_49_
+TTTAAAATGTCTATTAGCAGTGATGTTTGAACTAGTCTTTTGAGAAGTGTGAAGAGAACA
+GGAAAAGTCTGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGTATACAC
+ATTTCGGGGCTGAGAGGCTAAAATGAGAATGGCGCAGCGGACGGGGAAGGCTTCTCTGCA
+CACAGCTGCTGGGATCTGAG
+>F2YP0BU02GLX2B length=189 xy=2593_0801 region=2 run=R_2009_09_24_17_10_49_
+AGTAATAAATAAAATCAAGGCTGGGGAATTACTACCAAGCTAAGCTCTGAAATCCAAAGC
+AAGAATTTAATATTTCCATTTTTCTGGCCGTAATAACTTCGTATAGCATACATTATACGA
+AGTTATACGATATGCCGATATTGTTAGTTTTAAGACATCAGTAGACTGGTTTTTTTGCCA
+CCAGCTTCT
+>F2YP0BU02JDE7P length=88 xy=3726_1203 region=2 run=R_2009_09_24_17_10_49_
+GAATGGAATCATCCGTAATTGAATGGAAAGGAATGGAATGGAATGGAATGGAATGGAATG
+GAATGGAATGGAATGGAATGGAATGCGT
+>F2YP0BU02IZKK3 length=117 xy=3568_2149 region=2 run=R_2009_09_24_17_10_49_
+TTTGTAGGATTTTAAGAATCAACAAAATTTTCTTTAAAATAAATCATTGTGTCCCTGTGT
+GTTGAAGTATGGCTTTGGTCAGTCTGTATTTATGTTTTCTTCGAATTCTTCTTAGAA
+>F2YP0BU02IVEHV length=49 xy=3521_0145 region=2 run=R_2009_09_24_17_10_49_
+CGTTCCATTCCATTCCATTCCATTCCATTCCATTCCATTCTATTCGGTT
+>F2YP0BU02GJJC7 length=469 xy=2565_3129 region=2 run=R_2009_09_24_17_10_49_
+TTTTTCTAAAAGACATCTGAATAAGGAGTTCGTAATAACTTCGTATAGCATACATTATAC
+GAAGTTATACGATATTGTCTCTTTAAAAGCTTTAGTTCCTTTTTAAAAATCACACTTGGG
+TCATTATCAATGCTTTTTGCAAGCATCAGCTCTTTCTGGGTTTTAATTTGATGTAATTCA
+TTAGTGTTTCTGACACACCTTACAGGTTTGCACCACTCTCTGAAACTGCCCTTGATTGAG
+TAACCTCCTTGTTCACTTTTCTGACTTATTCTTCTAAAACCTGAGCTCTCCAGTGATTTT
+GGGAGATTTTACCCCTCATTGGTGACTTGAAGTTTCTTCTTCTTATCTTCTTTGCTAGAA
+TAACTTCTTGTTAAACAATCAGAACTCATTGTGTTTCCTCTCTTCTTCCTGAATCCTATT
+GGCTTTTATACATTTTAGGAGCAGAATTGAACTAAAGAATAAAACATGT
+>F2YP0BU02HLBKR length=61 xy=2996_0585 region=2 run=R_2009_09_24_17_10_49_
+CAATGGATTCAACTCGATTGCAATGGAATGGAATAGAATGGAATGGAATGGAATGGAATG
+G
+>F2YP0BU02IFSP4 length=259 xy=3343_1178 region=2 run=R_2009_09_24_17_10_49_
+TTCTTACACCAGCCACTCACTGGCTAGGAATGATGTCAAGAGACGGTTAGCCATCTCTTG
+GAATGCTTCTCAGCAGCAGTCTTACACTTGGAAAAATAGACTCGTTCCTTTCCCCATGGG
+CAAGAATAGATAACAAAAGAAATAAGCTATCAAAACAAGGGCAAAGTTGTCGTATAACTT
+CGTATAATGTATGCTATACGAAGTTATTACGAGAAGAATGTAGCACAAATTTCTTGAGGA
+AACACAAAGAACTTCATGC
+>F2YP0BU02HV3I0 length=372 xy=3118_3658 region=2 run=R_2009_09_24_17_10_49_
+TTTGTGGAAGTGGACATTTCGCGTAATAACTTCGTATAGCATACATTATACGAAGTTATA
+CGATCATCATCAAAATGTAGAGAGAAGCACTATTAGAAACTACTTGGTGATATCTGCATT
+CAAGTCACAGAGTTGAACATTCCCTTACTTTGAGCACGTTTGAAACACTCTTTTGGAAGA
+ATCTGGAAGTGGACATTTGGAGCGCTTTGATGCCTTTGGTGAAAAGGAAACGTCTTCCAA
+TAAAAGCCAGACAGAAGCATTCTCAGAAACTTGTTCGTGATGTGTGTACTCAACTAAAAG
+AGTTGAACCTTTCTATTGATAGAGCAGTTTTGAAACACTCTTTTTGTGGATTCTGCAAGT
+GGATATTTGGAT
+>F2YP0BU02GJRKA length=308 xy=2568_1464 region=2 run=R_2009_09_24_17_10_49_
+ATTGTGGTCAGAACAATACTCAATATAATTTAAATCTTATATTATTCAAGAATTGTTTGT
+GGCCTAACGTGTGATCTGTCCTAGAGATTGTCTCATGTGCAGTTGAGAAGAATGTACATT
+CTTCAGCTGTTGGATGGAATGTTTTGTATATGTCTGTTAGGTTCATTTGATCTAGAATGT
+AGATTAACTAGGATGTTGATTTATTTCTGTCTAGATGACAGAAAATTCTGGTCGTATAAC
+TTCGTATAATGTATGCTATACGAAGTTATTACGAATGATGCGCTTCAAAGAGTTGTCTTC
+TATGCTTT
+>F2YP0BU02I60SJ length=372 xy=3653_1585 region=2 run=R_2009_09_24_17_10_49_
+TTTTGAAGGAGCAGTTTTGAAACCCTCTTTTCTGGAATCTGCAAGAGTATATTTGCCTAG
+CCTTGAGGATTTCGTTGGAAACGGGATTGTCTTCAGATAAAATCTAGACAGAAGCATTCT
+CAGAAACTTCTTTGGGATGTTTGCATTCAAGTCACAGAGCAGAACATTCCCTTTGGTAGA
+GCAGGTTTGAAACACTCTTTTTTAGTATATGGAAGTGGACATTTGGAGCGCTTTCAGGCC
+TACGTTGGAAAAGGAAACGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGAG
+ATTTCGTTGGAAGCGGGAATTCGATACAAATTGCAGACTGCAGCGTTCTGAGAAACATCT
+TTGTGATGTTTG
+>F2YP0BU02FZ6UJ length=56 xy=2345_1561 region=2 run=R_2009_09_24_17_10_49_
+TTTTGTACCTGGTGAACGATGTGACTGTCTCACAGATTTTTAAAATATGTAATGAC
+>F2YP0BU02FYXT9 length=243 xy=2331_0575 region=2 run=R_2009_09_24_17_10_49_
+AGAAGAATTTCTGAGAATGCTGCTGTCTACCTTTATTTGAATTCCCGCTTCCAACGAATC
+CTCCAAGCTATCCAAATATCCACCTGCATTTTCCACAAAAGAGTGTTTCAAAACTGCTCT
+ATCAATAGAAATGTTTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGATG
+AAAGGGAATCTTCAACTCTATGAGTTGAAGGCAGACATCAGAAAGAAATTTCTGAGAATG
+CTG
+>F2YP0BU02GP5KL length=263 xy=2641_0547 region=2 run=R_2009_09_24_17_10_49_
+AACCAGAATGGATTGGAATATAATGGAGTGTAAGGGAATTGAATAGAATCAATCTGAATG
+TAATGAAAGGGAATGGAACTGAAGGGAATGGAATGGAATGGAATGGAATGGAATGCAATG
+GAATGGAATCAACCCGAGTGCAATCGAATGGAATACGGAATGGAAATGGTCGTAGTAACT
+TCGTATAATGTATGCTATACGAAGTTATTACGAATGGAGTCATCCGGAATGGAACAGAAA
+GGAATGGAATGGAATGAACTGAN
+>F2YP0BU02JGZBK length=296 xy=3766_3390 region=2 run=R_2009_09_24_17_10_49_
+TTTTGATGCCTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGAGATCATG
+GATATTCTGGAAATAAAGGCTTTCGAGTAGTATCTTGCATTTTTCTCAACAGATTTCAAG
+TGTTGAACCGTTATAGAGGAACAACGCAAAGGACTAAAATAGTCAAGTAAAGTTGTATGG
+ATGAGAAGAAATGCAACGAAGGGAGTTCATCAAAATGTAGTCTTCTAACCCACATTGGTT
+TGCTAGATAGCATTTAAATTTGAGAGCTTGACTTTGAGGTTGAATATTTAATTTCG
+>F2YP0BU02H0L6E length=52 xy=3170_1460 region=2 run=R_2009_09_24_17_10_49_
+ACATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGTGGAGAA
+>F2YP0BU02HOYJH length=292 xy=3037_2379 region=2 run=R_2009_09_24_17_10_49_
+TTACTTAACCTCTCTAGGCCAAACTTTCCTCATCTTTAAAGTGGGGTTAATAAAACTCCG
+CTTCTTATTATGAGGTCTAGATGAGAGAATGTTTGTGAAGTGCTTAACATGGTATGTGGA
+AAGACAGTATTCATTATTCATTAAATCATGACCTATTAGATAAAATAGTTTTTTAGAGGG
+GTTATGTGTGCTATGATTGTGGGAGTTTGGTGGAAGGGATTAACGTAATAACTTCGTATA
+GCATACATTATACGGAAGTTTATACGATGCAATTCAAGTGGAAGCTGTCTTC
+>F2YP0BU02GSQKZ length=282 xy=2670_2305 region=2 run=R_2009_09_24_17_10_49_
+AGATGGCCTTACAAGTATTGCTTTCTGCATTTTATTGAAGAGGAAATGAGACTCAAGGTA
+AATGACTGATTCAATGCCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGAC
+TTGAATTCCTGAGCTCAGTCCTCCACACTGCAAGTATTACAGGTGTGACCCACTCTGCAG
+CCAGTTTAGGTACTCTATCCTATTTTACAGTTGAAGAAACCGACACCTAGAGGGAAGGTA
+ATTTGCCCAGGTCACATGGCTAGTAATTGATGGGACTGGCAT
+>F2YP0BU02HNS0A length=234 xy=3024_1800 region=2 run=R_2009_09_24_17_10_49_
+AGTAGATAGGCAAGTTCTCTAGGAAATATTACTCATACAGCCTAAGAATGTTAATTTGGC
+TCTCCCTCACTGGCAAGGTAACAAGTCCGTAATAACTTCGCATAGCATACATTATACGAA
+GTTATACGAGAAATGTATTACATAGCCAAATACAGTATGTATAAAATATATATTGCAATA
+TTTCATACTTGTTAGTGAAAATATTTTTACAACGTAGTGCCTCCCAAGTGCAGG
+>F2YP0BU02G28U1 length=206 xy=2790_1035 region=2 run=R_2009_09_24_17_10_49_
+TAATATCTTATGAGTCAAGGACAAACCAAAGAGAAGCCAACAGCATTTTGAACTTCGTAT
+AACTTCGTATAATGTATGCTATACGAAGTTATTACGCTGGGCAACCACTAATCTGTTCTA
+CATCTCTATAGTTATGATATTTTATAAATGCTATATAAATGGAATCATGCAGCATGTATC
+CTTCCGACGATGACTTTTTAATCTCA
+>F2YP0BU02HU8CF length=278 xy=3109_0109 region=2 run=R_2009_09_24_17_10_49_
+ATGGAATGGAGTGGAATGGAATGGAATGGAATGGAACAACCCGAATGAAATGGAATGTAA
+TGGAGAGTAAGGGAGTTGAAAGAATCAATCCGAATGGAATGGAATGGAATGGAATGGAAT
+GGAACGGAATGGAATGGAATGGAATGGAATGGAATGGAATGCAATGGAATGGAATCAACC
+CGAGTACAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATCGTATAAACT
+TCGTATAAATGTATGCTATACGAAGTTATTACGAATGG
+>F2YP0BU02G140S length=444 xy=2777_2650 region=2 run=R_2009_09_24_17_10_49_
+TTTTACACCAGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGCCAAAAG
+CAATATCCAGTACATCATATGTCGCACATAAGTGTCATTTGCTGTTACTGTTTTTATTAT
+TATTATTAAAGATAAGGAGACTAGATAGGCTTTGAAAAATATATGATGAATTTGTTTTCA
+GTCACTTTGAGTGCTAAATAGAAATTCACTTCCTGAGTTTCTAATGATCGCCATTCTAAC
+TTGTGTGAGGTGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGC
+TGAGCATTTTTTATGTGTCTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGCTC
+ATATCCTTTGCCCACTTTTTGATGGGGTTGTTTGTTTTTCTTGTAAATTTGTTTGAGTTC
+ATTGTAGATTCTGGATATTAGCCC
+>F2YP0BU02HZ20Y length=299 xy=3164_1216 region=2 run=R_2009_09_24_17_10_49_
+ACCAGAGGCTCAAGATACCCAAGTAAATACCCAGGATTTCCAGGGAGAAGTAAAGCAAAG
+ACCTGGCAAGTGTTATCACTGCAGCCATAGTTAATTCAAATGTTCATGGATGCAACTTCA
+ACTATAGACATTTGACCACCTGTTATCGTATAACTTCGTATAATGTATGCTATACGAAGT
+TATTACGGTAAAGCACTGAGAGAAGCGACATTGGAGGAGAGAGAAGGAAGAGAGCCAAGA
+AGGATGAAGGCCCTCTGAGGAGTGAGATGCTTGGTGCTATTGGAAGGAGGATGGAGGGC
+>F2YP0BU02J3VA9 length=291 xy=4027_2227 region=2 run=R_2009_09_24_17_10_49_
+TTTGCTTTCCATTTTTGGCTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTAC
+GTCCACCATATTAACTGGCCTTATTAATTTCCTAGGGTTGCCATAACAAAGTACTGTGAA
+CTGGGTGGCATAAAACAGTACAAATTATTCTCATGGTTCTGGGGGCTAGAAGTCCAGAAT
+AAAGGTCTGATAGGATCATGTTCTCTGTGAAAGCAGTTAGAGGAGAATCCTTCCTTGTCT
+CTTTTGGGTTTCTTGTGATTGCCAGCGATCTTTGGTGTTCCTGGCTTGCAA
+>F2YP0BU02FW49S length=358 xy=2310_2910 region=2 run=R_2009_09_24_17_10_49_
+TTCCATTCAAGTCCATTCGCTTCCATTCCATTCCATTCCTTTCCATTCCGTGCCATTCCA
+TTCAATTCTATTCCATTCGACTCCATTCCATTCCATTGCCTTCCATCCGATTCCATTCCA
+TTCTATTCCTTTCCATTCCGTTCAATCACATCCCATTCTTTTCCATTATATTCGAGTCCA
+CTCCACTCCAGTACATTCCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA
+TTGCTTTCCCAGCCCATTGGCTTAATTCAGCCCTTAATGCTCTTCCCCTTTGGAATGCAG
+GTGGTTTAATGAGAATTTAGGTTCTCAAGTCAGATTGCCTGGGTTCACATCTAGCTTT
+>F2YP0BU02GWHIX length=297 xy=2713_1063 region=2 run=R_2009_09_24_17_10_49_
+TCTTTGGATGTTCCAGTAATGTATGTGTTCAATCCATTTGTCGGTCTTCCATAGTTCTCA
+TTTTCTCTGTAATACTTGAGTTTTGCTTTTCAGATGTTTGCTTAGATAATTTTGTATAAC
+GTAATAACTTCGTATAGCATACATTATACGAAGTTATACGACATCTTGCTTCTTAATTTA
+TTTTATTTTTAAATTTTATTTCATCTAGAGTTTACAATACACATCTTTAACTTATCACAG
+CTCTATGTAGAGTATAAAGAATGTACAGCAGGAGAAGTCAGTTTTTCTCTTCTGTCT
+>F2YP0BU02GIT1L length=445 xy=2557_3079 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTGTTTCCTCAGTTTTTCATTCCTCTGTTTCCCCCTTTCTACCTTCTGTGGGGTTA
+TTTGAACACATTTCTTATCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA
+GTGTTGGTATTATCTACATCTAAAAACAAAATTGGCATGGAAGTGGGAATAGAAAGAATG
+AGAAAAGAGGAGGCGAGAGGGTGGCTCAACAGTTGAGACAGGTTTTCAAGAGTAAACCTC
+AAAAGGGCTTCTGGCCAGCAGGGTCAGGAGCAAACTTTTCTATAGCCTGAGGCTTTTTAA
+AGGGCCCGGTGGGGAATTGTGCTTTGAAGCAAGATTCTATTAGGGAGGGTTTGGAGAAGT
+GCTGGCTGTTCTGTTAGGGCCATTATGCTCTGTTGAAGCTATGGGCAGGGGTGACATTCG
+GGGGTTCTGGGCCAGGGTGGCCAAA
+>F2YP0BU02IMSS7 length=364 xy=3423_0201 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTTGAGACGCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGATGTCA
+ACAAGGCGGCCCCCATAGGCTGGAGGCTATGCTCTGGAGAAGAGTGCACCTGTGAATTCT
+TGACAGAGACTGCTCAGCAGCTGCAGGATGGCTGCACCTCCCTGGTAAGGGAGGTCTATA
+TGTATCAACTGTTCTCAACCTTACAAAATATATTATTTTAACCCCAGTCTTCTAATACAG
+TTGCTTGCTGTATGTTTGGTCCTTAGCAAGACCAGCTTTCCAGAGCAGTGCCCAGGGCTG
+GCTCTAATCACATCACCTTCCTTCTTCCTATCACAATTATCCCCTCTGGATCTCATTTGT
+GGAT
+>F2YP0BU02JTR7A length=406 xy=3912_2676 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTTTTTTTTTTGAGGCGGAGTTTTCGCTCTTGTTGCCCAGGTGGGAGTGCAATGGT
+GCAATCTCAGCTCGCCACAACCTCCGCCTCCCGAGTTCAAGCGATTCTCCTACCTCAGCC
+TCCCAAATAGCTGGGATTACAGACATGCACCACCATTGCCTGGCTGATTTTGTATTTTTA
+GTAGAGACGGGGTTTCTCCACGTTGGTCAGGCTGGTCTCGAACTCTCGTATAACTTCGTA
+TAATGTATTGCTATACGAAGTTATTACGCCCAAAATTTACTAAATCAGAATATACATTTT
+AACAAGATTTCCCTGAGTGATTTCTATGCACATTAAAGTTTAAGTTGGTACATTTCTTGA
+CTGGGAATATTACTATGTTACTCGATATTGTCTGGCATGCTGTTAG
+>F2YP0BU02JHSQ4 length=341 xy=3776_0574 region=2 run=R_2009_09_24_17_10_49_
+AATCACTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCTAAGATCATGTCACTGCATTCCA
+GCTTGGGCAACAGAGACTCCATCTACAAAAAGTAAACTATATCCTTAGTCAAGTAATCCC
+ATCGTTAGAACTCTCTGGCCATCGTTCAGTCCGTAATAACTTCGTATAGCATACATTATA
+CGAAGTTATACGATAGCATAATTTGTGTATTTCCCTTAAAATATTAATTTTAATATCCTG
+TGCATCAGGCAGTTTCCTCAGCTCTTATTCTTTATCAGGAACCCTTCCCATGTCTTTTGG
+TTATGATGATATCATTGAATCTACTGGAGTCCAGCAGTGGC
+>F2YP0BU02GDLVC length=394 xy=2498_0870 region=2 run=R_2009_09_24_17_10_49_
+GAAGTAGCTGGGATTACAGGACATGAGCGCAACCAAGAGACATTTTTAAAGTACCAAGTT
+CCCAGGTTCCAATTCTAGACCTACTAAAAGGAAAATTATTCACTGGATGCTTTGGAGGTG
+CTAGACAGCCCTTCTAACACACACACCATGTGCTTTGCTTCCCAAGCACAATTCTCTAGC
+AATAAAAAGGGGACTGTCTAGAATACAACTTACCTGACAAATGATACTCTCTGGCTTGTT
+ACACGAACTATCCGTAATAACTTCGTATAGCATACATTATATGAAGTTATACGAGGATCA
+GCTGTTCACACCATCATGGCCAAGAAAGGCCAAAATAGCCATAGGACTTCTAGAATTTGT
+GGAAGATGTTTTCCAATGGCCACTACGGAAATTT
+>F2YP0BU02H1CSQ length=248 xy=3178_3192 region=2 run=R_2009_09_24_17_10_49_
+TTTCTTTCTAAGCTGAGAAGACCTTTATATATCATATATATAACATATAAATATATATAA
+TTTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGGATTGACCTGCCTCAG
+CCTCTCAAAGTGTTGAGATTACAGGCCTGAGCTTCTGCTCCCAGCCCACATCCCATTCTT
+GAACATTTAGATGTTCTTCTTTTCCTCCTATAAATAACACAAGTACACAGGAATTTATAA
+TGTCCTCT
+>F2YP0BU02GGAIJ length=65 xy=2528_3241 region=2 run=R_2009_09_24_17_10_49_
+TGTGATGATTGCATTCAAGTCACAGAATTGAACATTCCCTTCTACAGAGCAGGTTTGGTA
+AACAA
+>F2YP0BU02JS9DO length=291 xy=3906_2858 region=2 run=R_2009_09_24_17_10_49_
+ACATCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACGGTTCTACTCTGTGAC
+TTGAATGCAAACATCCCAAAGAAGTTTCTGAGAATGCTTCTGTCTAGATTTTCTCTGAAG
+ACAATCCCGTTTCCAACGAAATCCTCAAGGCTAGGCAAATATACTCTTGCAGATTCCAGA
+AAAAGAGTGTTTCAAAACTGCTCCTTCAAAACGGTGGTTCAATTCTCTTAGTTGAGTACA
+CACATCTCAAATTAGTTTCTGAGAATGCTTCTGCCTAGTTGTTACGGGAAG
+>F2YP0BU02GM4B1 length=165 xy=2606_2335 region=2 run=R_2009_09_24_17_10_49_
+TTTTGGAGCTCACAGAGTCCTATACTGAAAACTGAATATCCCACAATAAAACTAGAAAGA
+AGATTCCTGTTAAACTACTATGTGCGTAATAACTTCGTATAGCATACATTATACGAAGTT
+ATACGAGTTTGTGATGTGGGTATTCAGCTCATAAATTAAAACCTT
+>F2YP0BU02HGA3Q length=248 xy=2939_0164 region=2 run=R_2009_09_24_17_10_49_
+AGTTGTCTCTCTTTAAAGAGAGAGATGGCTGGTCACGGGGCTCCTGTCTGTAATCTCAGC
+GCTTCAGGAGGCTGAGCGGAAGGATCGCTTGAGATCAGGAGTTCAATACCATTCTGGGCA
+ACATAGCGAGACCCCTGACTCGACAGAAAAATACCAAACGTAATAACTTCGTATAGCATA
+CATTATACGAAGTTATACGAACTTATATGTGTTCTTTTGAGAAGTATCTGTTCATGTCCT
+TTGCTCAC
+>F2YP0BU02H0Y31 length=236 xy=3174_1839 region=2 run=R_2009_09_24_17_10_49_
+TCTGTGTCTGTTTGTTCTGTGCTGTATCCTAGAATTTAGCACAGTGCCTGGTATGTCAGA
+CATTACTAAATATAGATTGACTGAATGCAATGCCTATTAGATGAACTAGTGAATCGTNTA
+ACTTCGTATAATGTATGCTATACGAAGTTATTACGGAGGAGGTACAGCATTGACAATGTC
+TTTCTGAATTATCCTTATCTTTGGGAGGCAATCCTTATACCCTAGCTGCAGAGATA
+>F2YP0BU02IYXL2 length=83 xy=3561_1048 region=2 run=R_2009_09_24_17_10_49_
+CTTTCAACTAATGGTGCCAAGATAATTGGTAAGCTACATGTAGAATTACGAAACTGGATA
+ATCATCTCTCACCTTATACAAAA
+>F2YP0BU02HJR12 length=382 xy=2978_2360 region=2 run=R_2009_09_24_17_10_49_
+TTTACTTATAATGCCTAATACAATGTAAAGGCTGTGGAATAGTTGTAATACTATTGCATT
+TAAAATTCATTTTATTTTTAATTGTTGTAGCATTATTTTTGTTTCTGTTCTAAAATATTT
+TCAATCCACAGTTGAATACAGAACCTGCAGCTACAGAGGGCTGATTGTACATGAGAAACT
+TCAGAGGAAAATGAAGACACAGAAAGTAGTTGGTTCTAAGTGCTTACACACTAGGTTGAA
+CAAACAGTAGTCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGATGCAATA
+TGTAAATTACATGCAAGATTTCATTCACCCTTTACCATTTTAGTTCCAGCTGGTATTTGG
+GGTTTTGGAAAAGTCCAAAACT
+>F2YP0BU02F5BIN length=392 xy=2403_3325 region=2 run=R_2009_09_24_17_10_49_
+TTTTCATGGCAGTGCAGTTAATAATCCGTAAGAACAAATATTTTGTTTAAAATTACCTTT
+TGAAATAGCAAAACCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGATGTT
+AGGTAAGCTGGACTGAGGGACAAGGTCATGTCCTCATAGAAAAGTCACAAACCTCGCTGG
+CTAGTATCTGTGGTTCTGTAGTAGAGGCACTTCTCAGGGTGAAGAGGAGGTGGGTGTTGG
+CCTAGTCCCCAAGCCTTTTTAAATATACATATCAAATTATTAACACCAAAATGAGACATT
+GTTTTTGTTTTAGTTTTGTTTTAATTTTAGAAGTGGGATAGCGGAAAACCCAAAGTGATC
+ATCTGCTCTTAGCACAGAGCTAAGCGTCTAAG
+>F2YP0BU02I8G7G length=386 xy=3669_3978 region=2 run=R_2009_09_24_17_10_49_
+TTTTGCTTAAATACTCTTGGTAATATACTATATACATTATTAGTACACAGAGCAAAACAG
+AAACTGGGGAATCACTTGAGAAACATCATACGTAATAACTTCGTATAGCATACATTATAC
+GAAGTTATACGACGAGAACTACGTGATGCATACACAAGCTTCAATAGCCAATTCGATCAA
+GTGGAAGAAAGGGTATCAGTGATTGTAGATCAAATCAGTGAAATAAAGCGAGAAGGGAAG
+TTTAGAGAAAAAAGAGTAAAAAGAAATCAACAAAGCCTCCAAGAAATATGGGACTATGTA
+AAATGACCAAATCTACGTCTGATTGGTGTACCTGAAAGTGACAGGGAGCATGGAACCAAG
+ATGGAAAACACTCTTCAGGATATTAT
+>F2YP0BU02H927V length=466 xy=3278_1081 region=2 run=R_2009_09_24_17_10_49_
+TTTTTTCCTCTTCATTTCTTGGGGGAAGAAGGAACACAGCAAACAGTCACTATAGACAAT
+TATTTAGACATTTCTATTATTATTTAGGGAGAAATTAGGTCGTATAACTTCGTATAATGT
+ATGCTATACGAAGTTATTACGATTGATTTGAAACATTTTTTCTTTTGTAATATACCCATT
+TCATGTTACAGATCTCCCTCTGAGCACTTTTTAGATGATCTCACAAATTTGCATAAATTC
+TGTATTAATTTTTATATAGGTAACATATTTTCTAATTTTTCTTTTGATGTATTTCTTGAC
+ATATCCATGGATTATTTGAAGTATCATGTTTAACTTCTAAATATTTGGGAAATTTTTAGG
+GTATCTTTCTATTATTAATTTCTAATTTCATTCTGTTGTGGATAGACAACATATATTGTA
+TAATTTCAATCATTTTAACTTTACTGAAATTTGTTTTATTGTTACT
+>F2YP0BU02HOCK5 length=284 xy=3030_2599 region=2 run=R_2009_09_24_17_10_49_
+TTCCCATGGAGCACTGCATGGAAGCCCCAGGGGGCCGTACCCATGTCACCGGCACTCCAT
+GTGTGGGTGGAGATCTCCAACTCCAACAAAAGATAGAGCTCTCTTGGCAGGAATGACAAG
+TGACAAAGTTCTCTATCTTACCCCGTGCCTTAAAATGATCATCTGAGTGTCCCAGAGTAA
+ACAGTAGTATTTGTAAAAATAAAAATATATATTTTTCTATTGAATATGTATATATACGTA
+ATAACTTCGTATAGCATACATTATACGAAGTTATACGAATGACG
+>F2YP0BU02G2GAG length=146 xy=2781_0870 region=2 run=R_2009_09_24_17_10_49_
+CAACATGAAATCCTATTTTAAGATCCTAAACTTCAGTTTATAAACTCGTATAACTTCGTA
+TAATGTATGCTATACGAAGTTATTACGATAGGGTGATGTATATATCTATTTCTACCCTAA
+ATAAGGAAAGCTGCAACTTTTTTCTT
+>F2YP0BU02JVSW4 length=224 xy=3935_2710 region=2 run=R_2009_09_24_17_10_49_
+AGCAGGACTCAGAGTCTGGTGGAAAGATAATTTATATAATATTTATAATGTAATAATGAA
+TTAATACTACCTAAATTGAACCATACGTAATAACTTCGTATAGCATACATTATACGAAGT
+TATACGAGGCTCAGGCAGGATTATTTGAACCAGGAGATACCGGTGTCAGGAAAGCAAAAC
+CCAGCATTTTGGGAGGCTCAGGCAGGATTGTTTGAAACCAACTT
+>F2YP0BU02G47T9 length=277 xy=2812_2911 region=2 run=R_2009_09_24_17_10_49_
+AACAATGTGAATAGTTCTGAAATAATGTCGTATAACTTCGTATAATGTATGCTATACGAA
+GTTATTACGGGCTCTGTGGGAGATGCAGTGGAAGCTTCAATTAGCCAAGTGGAAGTTTCT
+ATTACAAATAAATAAGCATTTAGTTAATTTCTTAGCATAATGAATGTGGTTTTAGAGGTT
+TCAGGATATGCACTATTCAATTCTCATTAGCCTTTTTATTGTCATCTTTATTCATCAGTT
+GTGGTGCCACTTGCCATGTAATGTTTTCCTTCTATCC
+>F2YP0BU02GKDRF length=348 xy=2575_1561 region=2 run=R_2009_09_24_17_10_49_
+ATGATCACCACGAGTTACAGATTTCTTTGTTCCCTCTCCATTCCCACTGCTTCACTTGAC
+TAGCCTAATCCTTCCAAAGGAAACGTAATAACTTCGTATAGCATACATTATACGAAGTTA
+TACGATGCCTTAGTTTGATATTGTAAATATCACAATATCACAATTGTCACAACATTTACA
+ATATCAAAATAAGCCAGGAATACCAAAAATTAAACCCACATGTCAATTTGAGAAAAATTT
+ATAGGACTATGACATGCATTAATTTGTCTTCTAAAAAATCTTCCATTAAAGTGTTGTATT
+TTTTCTTTTGATTCCTTCATTACATCAGGCTCTGTCCTTGAATTCCTT
+>F2YP0BU02I6CRD length=70 xy=3645_3207 region=2 run=R_2009_09_24_17_10_49_
+ATTCTGACTATCCGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGATGGGCG
+GACTACTACT
+>F2YP0BU02G63QT length=232 xy=2834_0803 region=2 run=R_2009_09_24_17_10_49_
+ATAAACTAGTATGTTTCCGAGTCGTATAACTTCGTATAATGTATGCTATACGAAGTTATT
+ACGCTCTAGTTGTCTGCAATAAATAAATTATCTTGCTGCAAAGATGCAAAGCACATTAGA
+AATTCACCAATCATGTTCTATGGGAAAGTAATTTCAAGAGAGACAAAAAGGGAGATGGAT
+GTTAGAGAGGCAATCCAAAAATGTCTGATATACAAGACAATACACCTTCATC
+>F2YP0BU02GLOJ1 length=75 xy=2590_0767 region=2 run=R_2009_09_24_17_10_49_
+TTTCTGTAGTAACTGGAAGTGAACATTAGGACCGTAATAACTTCGTATAGCATACATTAT
+ACGAAGTTATACGAT
diff -r 765c454bcaa7 -r bb7c2b314e3e test-data/lastz_paired_input3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lastz_paired_input3.fasta Tue Mar 02 16:40:40 2010 -0500
@@ -0,0 +1,2 @@
+>linker
+TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG
diff -r 765c454bcaa7 -r bb7c2b314e3e test-data/lastz_paired_input4.qual454
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lastz_paired_input4.qual454 Tue Mar 02 16:40:40 2010 -0500
@@ -0,0 +1,700 @@
+>F2YP0BU02IPIOC length=313 xy=3454_0058 region=2 run=R_2009_09_24_17_10_49_
+14 14 14 16 16 24 24 30 38 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 32 32 32 32 40 40 40 40 40 40 40 40
+39 39 38 38 38 40 40 40 40 40 40 40 40 30 30 30 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 38 36 20 20 22 22 22 34 20 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 28 28 28 28 39 39 40 39 39
+39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 38 36 36 24 24 24 24 30 15 15 15 24 27 38 40 40 31 31 31 31 40 40 40 40 40 40 40 40 40
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+40 40 40 40 40 40 40 40 40 40 40 40 40
+>F2YP0BU02GASSR length=219 xy=2466_0953 region=2 run=R_2009_09_24_17_10_49_
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+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 30 30 30 33 35 34 40
+>F2YP0BU02HLXG3 length=220 xy=3003_0293 region=2 run=R_2009_09_24_17_10_49_
+40 40 40 40 39 39 39 34 34 19 16 16 36 40 40 36 27 19 19 19 30 30 36 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 35 21 21 21 30 30 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 34 40 40 40 40 40 40 24 20 20 19 19 28 33 38 36 36 36 36 36 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 36 36 40 40 40 30 30 20 20 20 33 36 34 34 34 34 36 40 31 33 33 34 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40
+40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+>F2YP0BU02GF6D7 length=134 xy=2527_1997 region=2 run=R_2009_09_24_17_10_49_
+40 40 40 40 40 40 40 40 39 30 21 21 21 30 30 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 34 34 34 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 39 39
+>F2YP0BU02G6NFT length=92 xy=2829_0151 region=2 run=R_2009_09_24_17_10_49_
+40 40 40 40 40 40 40 40 39 39 39 39 40 40 40 40 40 40 40 40 40 40 39 39 39 39 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 39
+39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+>F2YP0BU02GD65M length=129 xy=2504_3880 region=2 run=R_2009_09_24_17_10_49_
+13 13 13 14 14 14 14 14 14 13 13 18 27 27 25 18 18 22 13 14 14 22 15 17 27 24 30 35 32 32 35 35 38 40 40 36 36 28 28 28 33 40 40 37 37 37 37 39 40 39 40 37 37 37 40 39 40 40 39 39
+37 37 38 32 29 28 27 27 27 36 36 36 36 38 36 36 38 40 29 29 29 27 24 19 19 24 33 39 29 29 25 28 33 40 40 40 40 40 38 36 36 36 36 33 35 27 27 14 14 14 14 14 14 11 17 21 24 28 25 26
+27 19 19 22 22 22 29 29 32
+>F2YP0BU02GW28F length=318 xy=2720_0525 region=2 run=R_2009_09_24_17_10_49_
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+40 40 40 40 40 40 40 40 40 40 40 40 33 33 33 32 40 40
+>F2YP0BU02HKJIX length=388 xy=2987_1095 region=2 run=R_2009_09_24_17_10_49_
+29 29 29 29 39 40 40 40 40 40 40 40 31 31 31 31 39 19 21 21 21 39 40 40 40 40 40 40 40 40 40 40 39 39 39 40 34 34 34 34 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 39 39 30 30 30 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40
+40 40 40 40 26 26 26 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 35 30 30 30 39 40 40 40 40 40 40 40 40 40 39 39 39 38 38 38 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 30 30 30 40 40 40 40 40 40 40 40 40 40 40 40 30 30 30 35 40 40 40 40 40 40 39 39 39 40 40 40 39 38 38 39 39 40 40 39 39 39 40 40 39 39 39 40 40 39 39 40 40 40
+40 39 39 39 40 40 40 39 39 37 39 34 39 40 40 36 36 36 36 31 33 26 22 16 16 16 26 22 31 31 32 28 29 24 24 26 36 34 40 40 37 39 39 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40
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+20 12 12 12 12 12 26 28 20 20 20 20 24 35 33 40 29 29 35 35 35 34 34 40 40 40 40 40
+>F2YP0BU02H80VC length=67 xy=3266_0534 region=2 run=R_2009_09_24_17_10_49_
+37 37 37 37 37 37 37 37 37 37 37 39 35 35 37 39 37 38 37 37 37 33 32 29 29 32 30 29 27 19 15 15 15 19 19 27 24 24 25 25 25 27 27 29 32 25 25 25 24 32 33 33 33 33 31 31 31 28 29 26
+23 19 17 17 19 14 11
+>F2YP0BU02IO6IM length=284 xy=3450_0684 region=2 run=R_2009_09_24_17_10_49_
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+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 39 39 39 40 39 39 38 38 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 34 34 34 34 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 35 34 34 35 39
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 39 39 39 40 40 40 40 40 40 40 40 40 40 39 39
+>F2YP0BU02GU7ME length=113 xy=2698_3012 region=2 run=R_2009_09_24_17_10_49_
+39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 35 35 35 39 40 40 40 40 40 40 40 40 40 40 37 24 24 24 35 40 40 40 40 33 24 23 23 23 35 39 36 36 34 31 29 32 29 16 16 16 16 22 27 22 20
+20 22 28 25 30 27 29 23 23 22 22 17 17 15 18 26 36 33 33 28 28 28 33 35 31 32 32 35 35 38 37 32 32 27 27 27 36 40 40 40 40 40 40 40 40 36 33 33 34 33 39 36 36
+>F2YP0BU02HYBDH length=366 xy=3144_0643 region=2 run=R_2009_09_24_17_10_49_
+21 21 21 21 38 37 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 33 33 33 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 38 27 25 25 23 22 14 14 14 14 14 22 12 27 26 31 31 37 40 34 40 40 40 40
+40 40 40 25 25 25 40 19 19 19 19 36 36 25 38 40 40 36 36 31 36 36 36 36 36 29 29 18 20 20 20 36 29 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+28 28 27 27 19 19 19 23 20 20 18 18 18 29 31 29 38 36 36 36 33 34 34 40 34 34 30 30 30 30 38 36 36 38 38 38 33 33 33 25 25 25 30 27 32 32 34 34 33 36 40 40 40 34 34 35 21 21 21 22
+34 34 40 40 38 28 28 28 31 30 17 17 21 28 40 40 40 40 40 40 38 38 38 40 40 40 40 40 40 40 40 38 38 38 40 40 40 40 40 34 34 34 40 40 34 30 30 30 36 33 33 33 36 36 36 29 26 26 26 33
+33 36 36 33 29 31 28 33 33 36 31 32 31 31 31 31 31 29 29 23 23 23 23 36 36 36 40 40 40 36 36 36 36 36 36 40 36 36 34 34 33 33 36 36 36 36 32 33 33 36 36 36 36 36 36 36 38 38 36 36
+36 34 34 34 19 19
+>F2YP0BU02GS94E length=98 xy=2676_3052 region=2 run=R_2009_09_24_17_10_49_
+37 37 37 37 37 37 37 37 37 37 37 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 37 37 35 35 33 33 28 16 15 15 15 19 17 21 24 17 18 11 11 11 22 17 25 17 18 11 11 11 12 12 16 18
+>F2YP0BU02GFM2N length=339 xy=2521_1533 region=2 run=R_2009_09_24_17_10_49_
+26 26 21 21 21 21 21 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 35 26 21 21 21 26 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40
+40 34 34 34 34 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39
+39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 39 40 40 38 38 38 40 40 40 40 40 40 40 38 38 38 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39
+39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 39 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 30 30 30 35 40 40 40 40 39 39 39 39 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 35 34 34 34 34 40 40 40 40 40 40 40 40 40 40 35 34 34 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 39 39 36 40 40 36 36 39 39 39 39 39 39 39 39 39 40 40 40 39 39 39 35 35
+>F2YP0BU02H2R5T length=71 xy=3195_0127 region=2 run=R_2009_09_24_17_10_49_
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 34 33 31 31 31 30 26 26 26
+30 30 28 22 30 27 30 27 28 27 23
+>F2YP0BU02IENAS length=319 xy=3330_0738 region=2 run=R_2009_09_24_17_10_49_
+39 39 39 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 30 30 30 40 40 34 34 34 34 40 40 40 40 40 40 40 40 40 40 34 34 34 34 40 37 37 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 39 39 39 40 40 40 40 40 40 40 40 24 24
+24 24 24 39 39 39 40 40 36 36 36 40 40 40 40 24 24 24 24 24 40 40 40 40 40 40 40 40 40 34 34 34 34 40 35 27 33 33 35 35 35 17 17 17 17 17 17 17 17 19 17 17 33 31 31 36 40 32 32 32
+31 39 39 40 36 35 25 25 25 23 32 14 14 14 12 12 12 32 27 27 27 26 19 19 22 22 26 31 36 31 31 22 22 22 24 36 23 34 34 36 36 36 39 39 40 40 40 40 40 40 40 32 32 31 31 35 16 16 16 16
+36 36 16 13 13 36 36 36 36 36 36 36 36 36 36 28 30 30 33
+>F2YP0BU02HT2D7 length=41 xy=3095_3085 region=2 run=R_2009_09_24_17_10_49_
+37 37 35 33 32 32 32 23 16 15 15 15 15 15 15 15 22 27 30 30 30 31 31 33 35 37 34 36 28 27 27 37 35 33 33 33 31 29 28 29 29
+>F2YP0BU02H8REW length=269 xy=3263_0566 region=2 run=R_2009_09_24_17_10_49_
+40 40 40 40 39 39 39 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40
+40 40 40 39 39 39 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 36 38 40 40 26
+22 14 14 14 14 22 22 31 31 26 26 26 32 30 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 34 34 21 21 21 40 35 36 36 36 36 36 40 40 40 39 34 35 34 39 40 40 39 39 36 36 36 39 40 40 40 40 30 30 30 30 40 40 40 39 39 39 40 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 39 39 39 39 40 39 39 40 40 40 40 38 35 35 35 35 26 26
+>F2YP0BU02IAR6Y length=369 xy=3286_0680 region=2 run=R_2009_09_24_17_10_49_
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+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 39 35 35 21 21 21 21 35 34 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 33 33 33 39 39 40 40 40 40 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 36 20 20 20 20 34 34 35 35 33 33 34 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+40 40 40 39 39 39 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40
+40 40 40 40 39 39 39 39 38 38 36 40 40 40 40 36 39 30 30 33 33 31 31 39 39 35 40 40 40 30 31 29 28 40 36 36 32 28 24 22 12 12 12 12 20 12 12 12 12 12 18 18 21 21 18 11 11 11 12 14
+26 32 36 33 32 30 28 32 35 36 36 30 20 20 20 34 34 36 36 36 40 40 40 36 39 39 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 34 34 33 30 24 26 24 30 33 37 36
+33 33 33 40 40 40 34 34 35
+>F2YP0BU02I3TZY length=65 xy=3617_0268 region=2 run=R_2009_09_24_17_10_49_
+39 39 39 39 39 39 39 39 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 34 38 34 36 35 36 32 21 15 15 14 14 19 18 22 21 25 25 25 25 18 18 18 18
+22 18 21 18 18
+>F2YP0BU02JP6S8 length=265 xy=3871_2922 region=2 run=R_2009_09_24_17_10_49_
+36 33 33 40 40 40 26 24 24 16 16 16 16 26 26 20 27 16 16 31 31 36 40 40 40 40 40 40 34 34 38 34 39 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 26 26 26 39 40 40 40
+40 40 40 40 40 40 40 40 40 39 25 25 25 25 25 34 34 35 35 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 38 38 38 40 40
+40 40 40 40 40 31 31 31 31 40 40 40 40 40 39 39 39 40 40 40 40 39 39 38 39 39 39 40 40 40 40 40 40 40 40 39 39 39 39 39 39 40 40 40 40 26 26 26 30 21 21 21 40 40 40 40 40 40 40 40
+40 40 40 40 39 39 39 40 40 40 39 39 39 39 39 39 35 35 35 40 40 40 40 40 34 34 35 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 35 34 34 40 40
+40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+>F2YP0BU02IG2DL length=165 xy=3357_2999 region=2 run=R_2009_09_24_17_10_49_
+38 36 30 30 30 35 36 21 21 18 18 18 18 17 30 30 30 29 32 36 36 40 39 39 39 40 40 29 29 29 40 40 40 40 40 37 37 35 40 39 39 34 33 34 36 35 28 28 28 31 31 35 35 39 33 36 36 33 24 26
+26 37 39 40 40 40 39 39 40 40 40 40 40 40 40 40 40 37 28 28 27 30 36 28 28 28 20 20 14 17 14 14 14 28 17 23 23 25 12 12 14 19 19 14 16 24 24 30 30 30 31 31 39 40 39 39 39 40 40 40
+40 40 40 40 40 40 39 33 33 33 33 37 39 40 40 40 40 38 38 37 36 36 37 37 40 33 29 29 29 33 40 40 40 40 40 40 40 40 40 40 39 33 28 28 27
+>F2YP0BU02I6OA8 length=121 xy=3649_1794 region=2 run=R_2009_09_24_17_10_49_
+28 28 37 37 37 37 37 35 35 35 37 39 39 39 39 37 37 37 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 37 37 37 37 37 37 37 37
+37 37 37 37 37 37 37 36 31 31 31 37 37 37 37 37 37 37 37 37 37 37 37 37 37 35 35 32 28 28 28 27 26 23 23 23 17 19 19 24 24 24 23 27 32 32 32 32 31 30 30 30 29 24 21 18 13 11 13 18
+17
+>F2YP0BU02JHJNK length=351 xy=3773_1070 region=2 run=R_2009_09_24_17_10_49_
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diff -r 765c454bcaa7 -r bb7c2b314e3e test-data/lastz_paired_out1.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lastz_paired_out1.sam Tue Mar 02 16:40:40 2010 -0500
@@ -0,0 +1,2 @@
+F2YP0BU02F2LFK 65 chr21 9749451 255 331H34M1I7M * 0 0 TATCCACTTGCAGATTCCACGAAAACAGTGTTTCAAAAACTG EEEEEE<787@AAA/../:25////50EGE@CCI::@@@III
+F2YP0BU02GASSR 65 chr21 41805812 255 193H26M * 0 0 ATCATTGTTGTCTCTCCTGGTGGCAG IIIIIIIIIIIIIIIIIIH???BDCI
diff -r 765c454bcaa7 -r bb7c2b314e3e tool_conf.xml.sample
--- a/tool_conf.xml.sample Tue Mar 02 16:35:21 2010 -0500
+++ b/tool_conf.xml.sample Tue Mar 02 16:40:40 2010 -0500
@@ -203,6 +203,7 @@
</section>
<section name="NGS: Mapping" id="solexa_tools">
<tool file="sr_mapping/lastz_wrapper.xml" />
+ <tool file="sr_mapping/lastz_paired_reads_wrapper.xml" />
<tool file="sr_mapping/bowtie_wrapper.xml" />
<tool file="sr_mapping/bowtie_color_wrapper.xml" />
<tool file="sr_mapping/bwa_wrapper.xml" />
diff -r 765c454bcaa7 -r bb7c2b314e3e tools/sr_mapping/lastz_paired_reads_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/sr_mapping/lastz_paired_reads_wrapper.py Tue Mar 02 16:40:40 2010 -0500
@@ -0,0 +1,756 @@
+#! /usr/bin/python
+
+"""
+Runs Lastz paired read alignment process
+Written for Lastz v. 1.02.00.
+
+# Author(s): based on various scripts written by Bob Harris (rsharris(a)bx.psu.edu),
+# then tweaked to this form by Greg Von Kuster (greg(a)bx.psu.edu)
+
+This tool takes the following input:
+a. A collection of 454 paired end reads ( a fasta file )
+b. A linker sequence ( a very small fasta file )
+c. A reference genome ( nob, 2bit or fasta )
+
+and uses the following process:
+1. Split reads into mates: the input to this step is the read file XXX.fasta, and the output is three
+ files; XXX.short.fasta, XXX.long.fasta and XXX.mapping. The mapping file records the information necessary
+ to convert mate coordinates back into the original read, which is needed later in the process.
+
+2. Align short mates to the reference: this runs lastz against every chromosome. The input is XXX.short.fasta
+ and the reference genome, and the output is a SAM file, XXX.short.sam.
+
+3. Align long mates to the reference: this runs lastz against every chromosome. The input is XXX.long.fasta
+ and the reference genome, and the output is a SAM file, XXX.long.sam.
+
+4. Combine, and convert mate coordinates back to read coordinates. The input is XXX.mapping, XXX.short.sam and
+ XXX.long.sam, and the output is XXX.sam.
+
+usage: lastz_paired_reads_wrapper.py [options]
+ --ref_name: The reference name to change all output matches to
+ --ref_source: The reference is cached or from the history
+ --source_select: Use pre-set or cached reference file
+ --input1: The name of the reference file if using history or reference base name if using cached
+ --input2: The reads file to align
+ --input3: The sequencing linker file
+ --input4: The base quality score 454 file
+ --ref_sequences: The number of sequences in the reference file if using one from history
+ --output: The name of the output file
+ --lastz_seqs_file_dir: Directory of local lastz_seqs.loc file
+"""
+import optparse, os, subprocess, shutil, sys, tempfile, time
+from string import maketrans
+
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( 'bx-python' )
+from bx.seq.twobit import *
+from bx.seq.fasta import FastaReader
+from galaxy.util.bunch import Bunch
+from galaxy.util import string_as_bool
+
+# Column indexes for SAM required fields
+SAM_QNAME_COLUMN = 0
+SAM_FLAG_COLUMN = 1
+SAM_RNAME_COLUMN = 2
+SAM_POS_COLUMN = 3
+SAM_MAPQ_COLUMN = 4
+SAM_CIGAR_COLUMN = 5
+SAM_MRNM_COLUMN = 6
+SAM_MPOS_COLUMN = 7
+SAM_ISIZE_COLUMN = 8
+SAM_SEQ_COLUMN = 9
+SAM_QUAL_COLUMN = 10
+SAM_MIN_COLUMNS = 11
+# SAM bit-encoded flags
+BAM_FPAIRED = 1 # the read is paired in sequencing, no matter whether it is mapped in a pair
+BAM_FPROPER_PAIR = 2 # the read is mapped in a proper pair
+BAM_FUNMAP = 4 # the read itself is unmapped; conflictive with BAM_FPROPER_PAIR
+BAM_FMUNMAP = 8 # the mate is unmapped
+BAM_FREVERSE = 16 # the read is mapped to the reverse strand
+BAM_FMREVERSE = 32 # the mate is mapped to the reverse strand
+BAM_FREAD1 = 64 # this is read1
+BAM_FREAD2 = 128 # this is read2
+BAM_FSECONDARY = 256 # not primary alignment
+BAM_FQCFAIL = 512 # QC failure
+BAM_FDUP = 1024 # optical or PCR duplicate
+
+# Keep track of all created temporary files so they can be deleted
+global tmp_file_names
+tmp_file_names = []
+
+def stop_err( msg ):
+ sys.stderr.write( "%s" % msg )
+ sys.exit()
+
+def get_tmp_file_name( dir=None, suffix=None ):
+ """
+ Return a unique temporary file name that can be managed. The
+ file must be manually removed after use.
+ """
+ if dir and suffix:
+ tmp_fd, tmp_name = tempfile.mkstemp( dir=dir, suffix=suffix )
+ elif dir:
+ tmp_fd, tmp_name = tempfile.mkstemp( dir=dir )
+ elif suffix:
+ tmp_fd, tmp_name = tempfile.mkstemp( suffix=suffix )
+ os.close( tmp_fd )
+ tmp_file_names.append( tmp_name )
+ return tmp_name
+
+def run_command( command ):
+ proc = subprocess.Popen( args=command, shell=True, stderr=subprocess.PIPE, )
+ proc.wait()
+ stderr = proc.stderr.read()
+ proc.wait()
+ if stderr:
+ stop_err( stderr )
+
+def split_paired_reads( input2, combined_linker_file_name ):
+ """
+ Given a fasta file of allegedly paired end reads ( input2 ), and a list of intervals
+ showing where the linker is on each read ( combined_linker_file_name ), split the reads into left and right
+ halves.
+
+ The input intervals look like this. Note that they may include multiple intervals for the same read
+ ( which should overlap ), and we use the union of them as the linker interval. Non-overlaps are
+ reported to the user, and those reads are not processed. Starts are origin zero.
+
+ #name strand start len size
+ FG3OYDA05FTEES + 219 42 283
+ FG3OYDA05FVOLL + 263 41 416
+ FG3OYDA05FFL7J + 81 42 421
+ FG3OYDA05FOQWE + 55 42 332
+ FG3OYDA05FV4DW + 297 42 388
+ FG3OYDA05FWAQV + 325 42 419
+ FG3OYDA05FVLGA + 90 42 367
+ FG3OYDA05FWJ71 + 58 42 276
+
+ The output gives each half-sequence on a separate line, like this. This allows easy sorting of the
+ sequences by length, after the fact.
+
+ 219 FG3OYDA05FTEES_L TTTAGTTACACTTAACTCACTTCCATCCTCTAAATACGTGATTACCTTTC...
+ 22 FG3OYDA05FTEES_R CCTTCCTTAAGTCCTAAAACTG
+ """
+ # Bob says these should be hard-coded.
+ seq_len_lower_threshold = 17
+ short_mate_cutoff = 50
+ # We need to pass the name of this file back to the caller.
+ tmp_mates_file_name = get_tmp_file_name( suffix='mates.txt' )
+ mates_file = file( tmp_mates_file_name, "w+b" )
+ # Read the linker intervals
+ combined_linker_file = file( combined_linker_file_name, "rb" )
+ read_to_linker_dict = {}
+ i = 0
+ for i, line in enumerate( combined_linker_file ):
+ line = line.strip()
+ if line.startswith( "#" ):
+ continue
+ if line.find( '#' ) >= 0:
+ line = line.split( "#", 1 )[0].rstrip()
+ fields = line.split()
+ if len( fields ) != 4:
+ # TODO: Do we want to err out here or just skip the line?
+ stop_err( "Wrong number of fields ( must be 4 ) in line %d: %s" % ( i+1, line ) )
+ name, start, length, size = fields
+ start = int( start )
+ length = int( length )
+ size = int( size )
+ end = start + length
+ if end > size:
+ # TODO: Do we want to err out here or just skip the line?
+ stop_err( "Bad interval in line %d: %s" % ( i+1, line ) )
+ if name not in read_to_linker_dict:
+ read_to_linker_dict[ name ] = ( start, end, size )
+ continue
+ if read_to_linker_dict[ name ] == None:
+ # Read previously marked as non-overlapping intervals, so skip this sequence - see below
+ continue
+ ( s, e, sz ) = read_to_linker_dict[ name ]
+ if sz != size:
+ # This should never occur
+ # TODO: Do we want to err out here or just skip the line?
+ stop_err( "Inconsistent sizes for %s" % name )
+ if s > end or e < start:
+ # Non-overlapping intervals, so skip this sequence
+ read_to_linker_dict[ name ] = None
+ continue
+ read_to_linker_dict[ name ] = ( min( s, start ), max( e, end ), size )
+ combined_linker_file.close()
+ # We need to pass the name of this file back to the caller.
+ tmp_mates_mapping_file_name = get_tmp_file_name( suffix='mates.mapping' )
+ mates_mapping_file = file( tmp_mates_mapping_file_name, 'w+b' )
+ # Process the sequences
+ seqs = 0
+ fasta_reader = FastaReader( file( input2, 'rb' ) )
+ while True:
+ seq = fasta_reader.next()
+ if not seq:
+ break
+ seqs += 1
+ if seq.name not in read_to_linker_dict:
+ if seq.length > seq_len_lower_threshold:
+ mates_file.write( "%-3d %s %s\n" % ( seq.length, seq.name, seq.text ) )
+ read_to_linker_dict[ seq.name ] = ""
+ continue
+ if read_to_linker_dict[ seq.name ] == "":
+ # TODO: Do we want to err out here or just skip the line?
+ stop_err( "Multiple sequences named %s" % seq.name )
+ if read_to_linker_dict[ seq.name ] == None:
+ # Read previously marked as non-overlapping intervals, so skip this sequence - see above
+ continue
+ ( start, end, size ) = read_to_linker_dict[ seq.name ]
+ if seq.length != size:
+ # TODO: Do we want to err out here or just skip the line?
+ combined_linker_file.close()
+ mates_file.close()
+ mates_mapping_file.close()
+ stop_err( "Sequence disagrees with size for sequence %s, size: %s seq.length: %s" % ( seq.name, str( size ), str( seq.length ) ) )
+ left = seq.text[ :start ]
+ right = seq.text[ end: ]
+ left_is_small = len( left ) <= seq_len_lower_threshold
+ right_is_small = len( right ) <= seq_len_lower_threshold
+ if left_is_small and right_is_small:
+ continue
+ if not left_is_small:
+ mates_file.write( "%-3d %s %s\n" % ( len( left ), seq.name + "_L", left ) )
+ mates_mapping_file.write( "%s %s %s %s\n" % ( seq.name + "_L", seq.name, 0, size - start ) )
+ if not right_is_small:
+ mates_file.write( "%-3d %s %s\n" % ( len( right ), seq.name + "_R", right ) )
+ mates_mapping_file.write( "%s %s %s %s\n" % ( seq.name + "_R", seq.name, end, 0 ) )
+ read_to_linker_dict[ seq.name ] = ""
+ combined_linker_file.close()
+ mates_file.close()
+ mates_mapping_file.close()
+ # Create temporary files for short and long mates
+ tmp_mates_short_file_name = get_tmp_file_name( suffix='mates.short' )
+ tmp_mates_long_file_name = get_tmp_file_name( suffix='mates.long' )
+ tmp_mates_short = open( tmp_mates_short_file_name, 'w+b' )
+ tmp_mates_long = open( tmp_mates_long_file_name, 'w+b' )
+ i = 0
+ for i, line in enumerate( file( tmp_mates_file_name, 'rb' ) ):
+ fields = line.split()
+ seq_len = int( fields[0] )
+ seq_name = fields[1]
+ seq_text = fields[2]
+ if seq_len <= short_mate_cutoff:
+ tmp_mates_short.write( ">%s\n%s\n" % ( seq_name, seq_text ) )
+ else:
+ tmp_mates_long.write( ">%s\n%s\n" % ( seq_name, seq_text ) )
+ tmp_mates_short.close()
+ tmp_mates_long.close()
+ return tmp_mates_mapping_file_name, tmp_mates_file_name, tmp_mates_short_file_name, tmp_mates_long_file_name
+
+def align_mates( input1, ref_source, ref_name, ref_sequences, tmp_mates_short_file_name, tmp_mates_long_file_name ):
+ tmp_align_file_names = []
+ if ref_source == 'history':
+ # Reference is a fasta dataset from the history
+ # Create temporary files to contain the output from lastz executions
+ tmp_short_file_name = get_tmp_file_name( suffix='short_out' )
+ tmp_align_file_names.append( tmp_short_file_name )
+ tmp_long_file_name = get_tmp_file_name( suffix='long_out' )
+ tmp_align_file_names.append( tmp_long_file_name )
+ seqs = 0
+ fasta_reader = FastaReader( open( input1 ) )
+ while True:
+ # Read the next sequence from the reference dataset. Note that if the reference contains
+ # a small number of chromosomes this loop is ok, but in many cases the genome has a bunch
+ # of small straggler scaffolds and contigs and it is a computational waste to do each one
+ # of these in its own run. There is an I/O down side to running by subsets (even if they are
+ # one sequence per subset), compared to splitting the reference into sizes of 250 mb. With
+ # the subset action, lastz still has to read and parse the entire file for every run (this
+ # is true for fasta, but for .2bit files it can access each sequence directly within the file,
+ # so the overhead is minimal).
+ """
+ :> output_file (this creates the output file, empty)
+ while there are more sequences to align
+ find the next sequences that add up to 250M, put their names in farf.names
+ lastz ${refFile}[subset=farf.names][multi][unmask] ${matesPath}/${matesFile} ...
+ >> output_file
+ """
+ seq = fasta_reader.next()
+ if not seq:
+ break
+ seqs += 1
+ # Create a temporary file to contain the current sequence as input to lastz
+ tmp_in_fd, tmp_in_file_name = tempfile.mkstemp( suffix='seq_%d_in' % seqs )
+ tmp_in_file = os.fdopen( tmp_in_fd, 'w+b' )
+ tmp_in_file.write( '>%s\n%s\n' % ( seq.name, seq.text ) )
+ tmp_in_file.close()
+ # Align short mates
+ command = 'lastz %s[unmask]%s %s ' % ( tmp_in_file_name, ref_name, tmp_mates_short_file_name )
+ command += 'Z=1 --seed=1111111011111 --notrans --maxwordcount=90% --match=1,3 O=1 E=3 X=15 K=10 Y=12 L=18 --ambiguousn --noytrim --identity=95 --coverage=80 --continuity=95 --format=softsam- '
+ command += '>> %s' % tmp_short_file_name
+ run_command( command )
+ # Align long mates
+ command = 'lastz %s[unmask]%s %s ' % ( tmp_in_file_name, ref_name, tmp_mates_long_file_name )
+ command += 'Z=15 W=13 --notrans --exact=18 --maxwordcount=90% --match=1,3 O=1 E=3 Y=10 L=18 --ambiguousn --noytrim --identity=95 --coverage=90 --continuity=95 --format=softsam- '
+ command += '>> %s' % tmp_long_file_name
+ run_command( command )
+ # Remove the temporary file that contains the current sequence
+ os.remove( tmp_in_file_name )
+ else:
+ # Reference is a locally cached 2bit file, split lastz calls across number of chroms in 2bit file
+ tbf = TwoBitFile( open( input1, 'rb' ) )
+ for chrom in tbf.keys():
+ # Align short mates
+ tmp_short_file_name = get_tmp_file_name( suffix='short_vs_%s' % chrom )
+ tmp_align_file_names.append( tmp_short_file_name )
+ command = 'lastz %s/%s[unmask]%s %s ' % ( input1, chrom, ref_name, tmp_mates_short_file_name )
+ command += 'Z=1 --seed=1111111011111 --notrans --maxwordcount=90% --match=1,3 O=1 E=3 X=15 K=10 Y=12 L=18 --ambiguousn --noytrim --identity=95 --coverage=80 --continuity=95 --format=softsam- '
+ command += '> %s' % tmp_short_file_name
+ run_command( command )
+ # Align long mates
+ tmp_long_file_name = get_tmp_file_name( suffix='long_vs_%s' % chrom )
+ tmp_align_file_names.append( tmp_long_file_name )
+ command = 'lastz %s/%s[unmask]%s %s ' % ( input1, chrom, ref_name, tmp_mates_long_file_name )
+ command += 'Z=15 W=13 --notrans --exact=18 --maxwordcount=90% --match=1,3 O=1 E=3 Y=10 L=18 --ambiguousn --noytrim --identity=95 --coverage=90 --continuity=95 --format=softsam- '
+ command += '> %s' % tmp_long_file_name
+ run_command( command )
+ return tmp_align_file_names
+
+def paired_mate_unmapper( input2, input4, tmp_mates_mapping_file_name, tmp_align_file_name_list, output ):
+ """
+ Given a SAM file corresponding to alignments of *subsegments* of paired 'reads' to a reference sequence,
+ convert the positions on the subsegments to positions on the reads. Also (optionally) add quality values.
+
+ The input file is in SAM format, as shown below. Each line represents the alignment of a part of a read
+ to a reference sequence. Read pairs are indicated by suffixes in their names. Normally, the suffixes _L
+ and _R indicate the left and right mates of reads (this can be overridden with the --left and --right
+ options). Reads that were not mates have no suffix.
+
+ (SAM header lines omitted)
+ F2YP0BU02G7LK5_R 16 chr21 15557360 255 40M * 0 0 ATTTTATTCTCTTTGAAGCAATTGTGAATGGGAGTTTACT *
+ F2YP0BU02HXV58_L 16 chr21 15952091 255 40M6S * 0 0 GCAAATTGTGCTGCTTTAAACATGCGTGTGCAAGTATCTTtttcat *
+ F2YP0BU02HREML_R 0 chr21 16386077 255 33M5S * 0 0 CCAAAGTTCTGGGATTACAGGCGTGAGCCATCGcgccc *
+ F2YP0BU02IOF1F_L 0 chr21 17567321 255 7S28M * 0 0 taaagagAAGAATTCTCAACCCAGAATTTCATATC *
+ F2YP0BU02IKX84_R 16 chr21 18491628 255 22M1D18M9S * 0 0 GTCTCTACCAAAAAATACAAAAATTAGCCGGGCGTGGTGGcatgtctgt *
+ F2YP0BU02GW5VA_L 16 chr21 20255344 255 6S32M * 0 0 caagaaCAAACACATTCAAAAGCTAGTAGAAGGCAAGA *
+ F2YP0BU02JIMJ4_R 0 chr21 22383051 255 19M * 0 0 CCCTTTATCATTTTTTATT *
+ F2YP0BU02IXZGF_L 16 chr21 23094798 255 13M1I18M * 0 0 GCAAGCTCCACTTCCCGGGTTCACGCCATTCT *
+ F2YP0BU02IODR5_L 0 chr21 30935325 255 37M * 0 0 GAAATAAAGGGTATTCAATTAGGAAAAGAGGAAGTCA *
+ F2YP0BU02IMZBL_L 16 chr21 31603486 255 28M1D1M * 0 0 ATACAAAAATTAGCCGGGCACAGTGGCAG *
+ F2YP0BU02JA9PR_L 16 chr21 31677159 255 23M * 0 0 CACACCTGTAACCCCAGCACTTT *
+ F2YP0BU02HKC61_R 0 chr21 31678718 255 40M * 0 0 CACTGCACTCCAGCCTGGGTGACAAAGCAAGACTCTGTCT *
+ F2YP0BU02HKC61_R 0 chr21 31678718 255 40M * 0 0 CACTGCACTCCAGCCTGGGTGACAAAGCAAGACTCTGTCT *
+ F2YP0BU02HVA88 16 chr21 31703558 255 1M1D35M8S * 0 0 TGGGATTACAGGCGTGAGCTACCACACCCAGCCAGAgttcaaat *
+ F2YP0BU02JDCF1_L 0 chr21 31816600 255 38M * 0 0 AGGAGAATCGCTTGAACCCAGGAGGCAGAGGTTGCGGT *
+ F2YP0BU02GZ1GO_R 0 chr21 33360122 255 6S38M * 0 0 cctagaCTTCACACACACACACACACACACACACACACACACAC *
+ F2YP0BU02FX387_L 16 chr22 14786201 255 26M * 0 0 TGGATGAAGCTGGAAACCATCATTCT *
+ F2YP0BU02IF2NE_R 0 chr22 16960842 255 40M10S * 0 0 TGGCATGCACCTGTAGTCTCAGCTACTTGGGAGGCTGAGGtgggaggatc *
+ F2YP0BU02F4TVA 0 chr22 19200522 255 49M * 0 0 CCTGGGAGGCGGAGGTTGCAGTGAGCCGAGATCACGCCATTGCACTCCA *
+ F2YP0BU02HKC61_R 16 chr22 29516998 255 8S32M * 0 0 agacagagTCTTGCTTTGTCACCCAGGCTGGAGTGCAGTG *
+ F2YP0BU02FS4EM_R 0 chr22 30159364 255 29M * 0 0 CTCCTGCCTCAGCCTCCCGAGTAGTTGGG *
+ F2YP0BU02G197P_L 0 chr22 32044496 255 40M10S * 0 0 TTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTgaataatgcc *
+ F2YP0BU02FIING 16 chr22 45959944 255 3M1I11M1I26M * 0 0 AGCTATGGTACTGGCTATGAAAGCAGACACATAGACCAATGG *
+ F2YP0BU02GUB9L_L 16 chr22 49198404 255 16M1I20M * 0 0 CACCACGCTCGGCTAATTTTTGTATTTTTAGTAGAGA *
+
+ The user must provide a mapping file (which might better be called an unmapping file). This file is usually
+ created by split_paired_reads, and tells us how to map the subsegments back to original coordinates in a single
+ read (this means the left and right mates were part of a single read). The mapping file contains four columns.
+ The first two give the mates's name (including the suffix) and the read name. The last two columns describe how
+ much of the full original sequence is missing from the mate. For example, in the read below, the left mate is
+ missing 63 on the right (42 for the linker and 21 for the right half). The right mate is missing 339 on the left.
+
+ left half: TTTCAACATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCA
+ AAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAGGCCTTCGGC
+ AAAATTCAACAAAACTCCATGCTAAAACTCTCAATAAGGTATTGATGGGA
+ CATGCCGCATAATAATAAGACATATCTATGACAAACCCACAGCCAATATC
+ ATGCTGAATGCACAAAAATTGGAAGCATTCCCTTTGAAAACTGGCACAAG
+ ACTGGGATGCCCTCTCTCACAACTCCTATTCAACATAGTGTTGGAAG
+ linker: CGTAATAACTTCGTATAGCATACATTATACGAAGTCATACGA
+ right half: CTCCTGCCTCAGCCTCCCGAG
+
+ mate_name read_name offset_to_start offset_from_end
+ F2YP0BU02FS4EM_L F2YP0BU02FS4EM 0 71
+ F2YP0BU02FS4EM_R F2YP0BU02FS4EM 339 0
+
+ The user can also specify a quality scores file, which should look something like this. Quality values are presumed
+ to be PHRED scores, written in space-delimited decimal.
+
+ >F2YP0BU02FS4EM
+ 38 38 38 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 38 21 21 21 40
+ 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 33
+ 32 32 40 40 40 21 21 18 18 21 34 34 31 40 40 40 40 40 40 40 40 40 40 40 40
+ 40 40 40 40 40 40 40 40 40 40 40 32 32 32 32 40 40 40 40 40 40 40 34 34 35
+ 31 31 28 28 33 33 33 36 36 36 17 17 17 19 26 36 36 36 40 40 40 40 40 33 34
+ 34 34 39 39 39 40 40 40 40 40 33 33 34 34 40 40 40 40 40 40 40 39 39 39 40
+ 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+ 40 40 40 40 40 40 40 39 39 39 39 39 39 40 40 40 39 39 39 40 40 40 40 40 40
+ 40 40 40 40 40 40 40 40 40 40 40 40 40 26 26 26 26 26 40 40 38 38 37 35 33
+ 36 40 19 17 17 17 17 19 19 23 30 20 20 20 23 35 40 36 36 36 36 36 36 36 36
+ 39 40 34 20 27 27 35 39 40 37 40 40 40 40 40 40 40 40 40 40 34 34 35 39 40
+ 40 40 40 40 40 40 39 39 39 40 40 40 40 36 36 32 32 28 28 29 30 36 40 30 26
+ 26 26 34 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39
+ 40 39 35 34 34 40 40 40 40 30 30 30 35 40 40 40 40 40 39 39 36 40 40 40 40
+ 39 39 39 39 30 30 28 35 35 39 40 40 40 40 40 35 35 35
+ >F2YP0BU02G197P
+ 40 40 40 40 40 40 40 40 40 40 39 39 39 39 39 39 40 40 40 40 40 40 40 40 40
+ 40 40 40 40 26 26 26 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+ 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+ 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+ 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 34 34 34 40 40
+ 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40
+ 40 40 40 40 40 40 40 34 34 34 34 40 40 40 40 34 34 34 34 40 40 40 40 40 40
+ 40 40 40 40 40 39 39 39 34 34 34 34 40 40 40 40 39 39 25 25 26 39 40 40 40
+ 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+ 33 33 33 33 40 35 21 21 21 30 38 40 40 40 40 40 40 40 40 35 35 30 30 30 40
+ 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
+ 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40
+ 40 40 40 39 39 39 40 40
+ >F2YP0BU02FIING
+ 32 32 32 25 25 25 25 24 25 30 31 30 27 27 27 28 28 21 19 19 13 13 13 14 19
+ 19 17 19 16 16 25 28 22 21 17 17 18 25 24 25 25 25
+
+ The output file is also SAM:
+
+ (SAM header lines omitted)
+ F2YP0BU02G7LK5 81 chr21 15557360 255 40M303H * 0 0 ATTTTATTCTCTTTGAAGCAATTGTGAATGGGAGTTTACT D>>>>IIIIIIHHG???IIIIIIIIIHHHFFEIH999HII
+ F2YP0BU02HXV58 145 chr21 15952091 255 226H40M6S * 0 0 GCAAATTGTGCTGCTTTAAACATGCGTGTGCAAGTATCTTtttcat AA===DDDDAAAAD???:::ABBBBBAAA:888ECF;F>>>?8??@
+ F2YP0BU02HREML 65 chr21 16386077 255 320H33M5S * 0 0 CCAAAGTTCTGGGATTACAGGCGTGAGCCATCGcgccc HH???HHIIIHFHIIIIIIICDDHHIIIIIIHHHHHHH
+ F2YP0BU02IOF1F 129 chr21 17567321 255 7S28M409H * 0 0 taaagagAAGAATTCTCAACCCAGAATTTCATATC 4100<<A>4113:<EFGGGFFFHHHHHHDFFFFED
+ F2YP0BU02IKX84 81 chr21 18491628 255 22M1D18M9S341H * 0 0 GTCTCTACCAAAAAATACAAAAATTAGCCGGGCGTGGTGGcatgtctgt ;;;=7@.55------?2?11112GGB=CCCCDIIIIIIIIIHHHHHHII
+ F2YP0BU02GW5VA 145 chr21 20255344 255 286H6S32M * 0 0 caagaaCAAACACATTCAAAAGCTAGTAGAAGGCAAGA IIIIIIIHHHIIIIIIICCCCIIIIIIIIIIIIIIIII
+ F2YP0BU02JIMJ4 65 chr21 22383051 255 208H19M * 0 0 CCCTTTATCATTTTTTATT 555544E?GE113344I22
+ F2YP0BU02IXZGF 145 chr21 23094798 255 291H13M1I18M * 0 0 GCAAGCTCCACTTCCCGGGTTCACGCCATTCT IIIIIIIIIIIGG;;;GGHIIIIIGGGIIIII
+ F2YP0BU02IODR5 129 chr21 30935325 255 37M154H * 0 0 GAAATAAAGGGTATTCAATTAGGAAAAGAGGAAGTCA 6...7/--..,30;9<<>@BFFFAAAAHIIIIIH@@@
+ F2YP0BU02IMZBL 145 chr21 31603486 255 342H28M1D1M * 0 0 ATACAAAAATTAGCCGGGCACAGTGGCAG BB1552222<<>9==8;;?AA=??A???A
+ F2YP0BU02JA9PR 145 chr21 31677159 255 229H23M * 0 0 CACACCTGTAACCCCAGCACTTT IIIIIIIIIIICCCCIIIIIHHH
+ F2YP0BU02HKC61 65 chr21 31678718 255 300H40M * 0 0 CACTGCACTCCAGCCTGGGTGACAAAGCAAGACTCTGTCT AA@BD:::==AAA@A?8888:<90004<>>?><<<<4442
+ F2YP0BU02HKC61 65 chr21 31678718 255 300H40M * 0 0 CACTGCACTCCAGCCTGGGTGACAAAGCAAGACTCTGTCT AA@BD:::==AAA@A?8888:<90004<>>?><<<<4442
+ F2YP0BU02HVA88 16 chr21 31703558 255 1M1D35M8S * 0 0 TGGGATTACAGGCGTGAGCTACCACACCCAGCCAGAgttcaaat >8888DFFHHGFHHHH@@?@?DDC96666HIIIFFFFFFFFFFF
+ F2YP0BU02JDCF1 129 chr21 31816600 255 38M103H * 0 0 AGGAGAATCGCTTGAACCCAGGAGGCAGAGGTTGCGGT IIIIIIIIIIIHHHIIHHHIIIIIIIIIIIIIIIIIII
+ F2YP0BU02GZ1GO 65 chr21 33360122 255 76H6S38M * 0 0 cctagaCTTCACACACACACACACACACACACACACACACACAC BBBBD?:688CFFFFFFFFFFFFFFFFFFFFFFFFFFDDBBB51
+ F2YP0BU02FX387 145 chr22 14786201 255 201H26M * 0 0 TGGATGAAGCTGGAAACCATCATTCT IIHHHHHHHHHHHHHFFFFFFFFFFF
+ F2YP0BU02IF2NE 65 chr22 16960842 255 209H40M10S * 0 0 TGGCATGCACCTGTAGTCTCAGCTACTTGGGAGGCTGAGGtgggaggatc BAAADDDDFDDDDDDBBA889<A?4444000@<>AA?9444;;8>77<7-
+ F2YP0BU02F4TVA 0 chr22 19200522 255 49M * 0 0 CCTGGGAGGCGGAGGTTGCAGTGAGCCGAGATCACGCCATTGCACTCCA FFF???FFFFFIIIIIIIIIIIIIIIIIIIIIIIHHIIFHFFFGDDB=5
+ F2YP0BU02HKC61 81 chr22 29516998 255 8S32M300H * 0 0 agacagagTCTTGCTTTGTCACCCAGGCTGGAGTGCAGTG 2444<<<<>?>><40009<:8888?A@AAA==:::DB@AA
+ F2YP0BU02FS4EM 65 chr22 30159364 255 339H29M * 0 0 CTCCTGCCTCAGCCTCCCGAGTAGTTGGG IIIIHHEIIIIHHHH??=DDHIIIIIDDD
+ F2YP0BU02G197P 129 chr22 32044496 255 40M10S258H * 0 0 TTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTgaataatgcc IIIIIIIIIIHHHHHHIIIIIIIIIIIII;;;IIIIIIIIIIIIIIIIII
+ F2YP0BU02FIING 16 chr22 45959944 255 3M1I11M1I26M * 0 0 AGCTATGGTACTGGCTATGAAAGCAGACACATAGACCAATGG :::9:32267=:114244/...446==<<<?@?:9::::AAA
+ F2YP0BU02GUB9L 145 chr22 49198404 255 176H16M1I20M * 0 0 CACCACGCTCGGCTAATTTTTGTATTTTTAGTAGAGA IIIIIIIIIHAAC;<</////@4F5778;IIIIIIII
+
+ """
+ left_suffix = "_L"
+ right_suffix = "_R"
+ # Read the mapping
+ mate_to_read_dict = {}
+ i = 0
+ for i, line in enumerate( file( tmp_mates_mapping_file_name, 'rb' ) ):
+ line = line.strip()
+ if not line.startswith( "#" ):
+ fields = line.split()
+ if len( fields ) != 4:
+ stop_err( "Incorrect number of fields (must be 4) in line %s of file %s" % ( i+1, tmp_mates_mapping_file_name ) )
+ mate_name, read_name, s_offset, e_offset = fields
+ if mate_name in mate_to_read_dict:
+ stop_err( "%s is in the mate_to_read_dict when it should not be." % mate_name )
+ mate_to_read_dict[ mate_name ] = ( read_name, int( s_offset ), int( e_offset ) )
+ # Read sequence data
+ read_to_nucs_dict = {}
+ seqs = 0
+ fasta_reader = FastaReader( file( input2, 'rb' ) )
+ while True:
+ seq = fasta_reader.next()
+ if not seq:
+ break
+ seqs += 1
+ seq_text_upper = seq.text.upper()
+ if seq.name in read_to_nucs_dict:
+ if seq_text_upper != read_to_nucs_dict[ seq.name ]:
+ # TODO: Should we err out here or just skip the line?
+ stop_err( "Inconsistent reads named %s (second occurs at line %d in file %s)" % ( seq.name, seqs, input2 ) )
+ #continue
+ read_to_nucs_dict[ seq.name ] = seq_text_upper
+ # Read quality data
+ def quality_sequences( f ):
+ seq_name = None
+ seq_quals = None
+ line_number = 0
+ for line in f:
+ line_number += 1
+ line = line.strip()
+ if line.startswith( ">" ):
+ if seq_name != None:
+ yield ( seq_name, seq_quals, seq_line )
+ seq_name = sequence_name( line )
+ seq_line = line_number
+ seq_quals = []
+ elif seq_name is None:
+ stop_err( "First quality sequence has no header" )
+ else:
+ seq_quals += [ int( q ) for q in line.split() ]
+ if seq_name is not None:
+ yield ( seq_name, seq_quals, seq_line )
+ def sequence_name( s ):
+ s = s[ 1: ].strip()
+ if not s:
+ return ""
+ else:
+ return s.split()[ 0 ]
+ read_to_quals_dict = {}
+ # TODO: should we use Dan's fastaNamedReader here?
+ for seq_name, quals, line_number in quality_sequences( file( input4 ) ):
+ quals = samify_phred_scores( quals )
+ if seq_name in read_to_quals_dict:
+ if quals != read_to_quals_dict[ seq_name ]:
+ stop_err( "Inconsistent quality sequences named %s (second occurs at line %d in %s)" % ( seq_name, line_number, input4 ) )
+ continue
+ if len( quals ) != len( read_to_nucs_dict[ seq_name ] ):
+ stop_err( "Inconsistent read/quality lengths for %s, quals: %s, read_to_nucs_dict[ seq_name ]: %s" % \
+ ( seq_name, quals, read_to_nucs_dict[ seq_name ] ) )
+ read_to_quals_dict[ seq_name ] = quals
+ # process the SAM file
+ tmp_align_file_names = ' '.join( tmp_align_file_name_list )
+ combined_chrom_file_name = get_tmp_file_name( suffix='combined_chrom' )
+ command = 'cat %s | grep -v "^@" | sort -k 1 > %s' % ( tmp_align_file_names, combined_chrom_file_name )
+ run_command( command )
+ fout = file( output, 'w+b' )
+ has_non_header = False
+ i = 0
+ for i, line in enumerate( file( combined_chrom_file_name, 'rb' ) ):
+ line = line.strip()
+ if line.startswith( "@" ):
+ if has_non_header:
+ stop_err( "Input SAM contains headers in several places (e.g., line %d) in file %s" % ( i+1, combined_chrom_file_name ) )
+ fout.write( "%s\n" % line )
+ continue
+ has_non_header = True
+ fields = line.split()
+ num_fields = len( fields )
+ if num_fields < SAM_MIN_COLUMNS:
+ stop_err( "Not enough columns at line %d (%d, expected %d)" % ( i+1, num_fields, SAM_MIN_COLUMNS ) )
+ # Set flags for mates
+ try:
+ flag = int( fields[ SAM_FLAG_COLUMN ] )
+ except ValueError:
+ stop_err( "Bad SAM flag at line %d: %s" % ( i+1, line ) )
+ if not( flag & ( BAM_FPAIRED + BAM_FREAD1 + BAM_FREAD2 ) == 0 ):
+ stop_err( "SAM flag indicates reads already paired, at line %d\n%s" % ( i+1, line ) )
+ mate_name = fields[ SAM_QNAME_COLUMN ]
+ unmap_it = False
+ half = None
+ if mate_name.endswith( left_suffix ):
+ flag += BAM_FPAIRED + BAM_FREAD2
+ fields[ SAM_FLAG_COLUMN ] = "%d" % flag
+ unmap_it = True
+ half = "L"
+ elif mate_name.endswith( right_suffix ):
+ flag += BAM_FPAIRED + BAM_FREAD1
+ fields[ SAM_FLAG_COLUMN ] = "%d" % flag
+ unmap_it = True
+ half = "R"
+ on_plus_strand = ( flag & BAM_FREVERSE == 0 )
+ # Convert position from mate to read by adding clipping to cigar
+ if not unmap_it:
+ read_name = mate_name
+ else:
+ try:
+ read_name, s_offset, e_offset = mate_to_read_dict[ mate_name ]
+ except KeyError:
+ stop_err( "'%s' doesn't appear in the mapping file." % mate_name )
+ cigar = fields[ SAM_CIGAR_COLUMN ]
+ cigar_prefix = None
+ cigar_suffix = None
+ if half == "L":
+ if on_plus_strand:
+ if s_offset > 0:
+ cigar_prefix = ( s_offset, "S" )
+ if e_offset > 0:
+ cigar_suffix = ( e_offset, "H" )
+ else:
+ if e_offset > 0:
+ cigar_prefix = ( e_offset, "H" )
+ if s_offset > 0:
+ cigar_suffix = ( s_offset, "S" )
+ elif half == "R":
+ if on_plus_strand:
+ if s_offset > 0:
+ cigar_prefix = ( s_offset, "H" )
+ if e_offset > 0:
+ cigar_suffix = ( e_offset, "S" )
+ else:
+ if e_offset > 0:
+ cigar_prefix = ( e_offset, "S" )
+ if s_offset > 0:
+ cigar_suffix = ( s_offset, "H" )
+ else:
+ if on_plus_strand:
+ if s_offset > 0:
+ cigar_prefix = ( s_offset, "S" )
+ if e_offset > 0:
+ cigar_suffix = ( e_offset, "S" )
+ else:
+ if e_offset > 0:
+ cigar_prefix = ( e_offset, "S" )
+ if s_offset > 0:
+ cigar_suffix = ( s_offset, "S" )
+ if cigar_prefix != None:
+ count, op = cigar_prefix
+ cigar = prefix_cigar( "%d%s" % ( count, op ), cigar )
+ if op == "S":
+ refPos = int( fields[ SAM_POS_COLUMN ] ) - count
+ fields[ SAM_POS_COLUMN ] = "%d" % refPos
+ if cigar_suffix != None:
+ count, op = cigar_suffix
+ cigar = suffix_cigar( cigar,"%d%s" % ( count, op) )
+ fields[ SAM_QNAME_COLUMN ] = read_name
+ fields[ SAM_CIGAR_COLUMN ] = cigar
+ # Fetch sequence and quality values, and flip/clip them
+ if read_name not in read_to_nucs_dict:
+ stop_err( "Missing sequence for '%s'" % read_name )
+ nucs = read_to_nucs_dict[ read_name ]
+ if not on_plus_strand:
+ nucs = reverse_complement( nucs )
+ quals = None
+ if read_to_quals_dict != None:
+ if read_name not in read_to_quals_dict:
+ stop_err( "Missing quality values for '%s'" % read_name )
+ quals = read_to_quals_dict[ read_name ]
+ if not on_plus_strand:
+ quals = reverse_string( quals )
+ cigar = split_cigar( fields[ SAM_CIGAR_COLUMN ] )
+ nucs, quals = clip_for_cigar( cigar, nucs, quals )
+ fields[ SAM_SEQ_COLUMN ] = nucs
+ if quals != None:
+ fields[ SAM_QUAL_COLUMN ] = quals
+ # Output the line
+ fout.write( "%s\n" % "\t".join( fields ) )
+ fout.close()
+
+def prefix_cigar( prefix, cigar ):
+ ix = 0
+ while cigar[ ix ].isdigit():
+ ix += 1
+ if cigar[ ix ] != prefix[ -1 ]:
+ return prefix + cigar
+ count = int( prefix[ :-1 ] ) + int( cigar[ :ix ] )
+ return "%d%s%s" % ( count, prefix[ -1 ], cigar[ ix+1: ] )
+
+def suffix_cigar( cigar, suffix ):
+ if cigar[ -1 ] != suffix[ -1 ]:
+ return cigar + suffix
+ ix = len( cigar ) - 2
+ while cigar[ix].isdigit():
+ ix -= 1
+ ix += 1
+ count = int( cigar[ ix:-1 ] ) + int( suffix[ :-1 ] )
+ return "%s%d%s" % ( cigar[ :ix ], count, suffix[ -1 ] )
+
+def split_cigar( text ):
+ fields = []
+ field = []
+ for ch in text:
+ if ch not in "MIDHS":
+ field += ch
+ continue
+ if field == []:
+ raise ValueError
+ fields += [ ( int( "".join( field ) ), ch ) ]
+ field = []
+ if field != []:
+ raise ValueError
+ return fields
+
+def clip_for_cigar( cigar, nucs, quals ):
+ # Hard clip prefix
+ count, op = cigar[0]
+ if op == "H":
+ nucs = nucs[ count: ]
+ if quals != None:
+ quals = quals[ count: ]
+ count, op = cigar[ 1 ]
+ # Soft clip prefix
+ if op == "S":
+ nucs = nucs[ :count ].lower() + nucs[ count: ]
+ # Hard clip suffix
+ count,op = cigar[ -1 ]
+ if op == "H":
+ nucs = nucs[ :-count ]
+ if quals != None:
+ quals = quals[ :-count ]
+ count, op = cigar[ -2 ]
+ # Soft clip suffix
+ if op == "S":
+ nucs = nucs[ :-count ] + nucs[ -count: ].lower()
+ return nucs, quals
+
+def samify_phred_scores( quals ):
+ """
+ Convert a decimal list of phred base-quality scores to a sam quality string.
+ Note that if a quality is outside the dynamic range of sam's ability to
+ represent it, we clip the value to the max allowed. SAM quality scores
+ range from chr(33) to chr(126).
+ """
+ if min( quals ) >= 0 and max( quals ) <= 126-33:
+ return "".join( [ chr( 33 + q ) for q in quals ] )
+ else:
+ return "".join( [ chr( max( 33, min( 126, 33+q ) ) ) for q in quals ] )
+
+def reverse_complement( nucs ):
+ complementMap = maketrans( "ACGTacgt", "TGCAtgca" )
+ return nucs[ ::-1 ].translate( complementMap )
+
+def reverse_string( s ):
+ return s[ ::-1 ]
+
+def __main__():
+ # Parse command line
+ # input1: a reference genome ( 2bit or fasta )
+ # input2: a collection of 454 paired end reads ( a fasta file )
+ # input3: a linker sequence ( a very small fasta file )
+ # input4: a base quality score 454 file ( qual454 )
+ parser = optparse.OptionParser()
+ parser.add_option( '', '--ref_name', dest='ref_name', help='The reference name to change all output matches to' )
+ parser.add_option( '', '--ref_source', dest='ref_source', help='The reference is cached or from the history' )
+ parser.add_option( '', '--ref_sequences', dest='ref_sequences', help='Number of sequences in the reference dataset' )
+ parser.add_option( '', '--source_select', dest='source_select', help='Use pre-set or cached reference file' )
+ parser.add_option( '', '--input1', dest='input1', help='The name of the reference file if using history or reference base name if using cached' )
+ parser.add_option( '', '--input2', dest='input2', help='The 454 reads file to align' )
+ parser.add_option( '', '--input3', dest='input3', help='The sequencing linker file' )
+ parser.add_option( '', '--input4', dest='input4', help='The base quality score 454 file' )
+ parser.add_option( '', '--output', dest='output', help='The output file' )
+ parser.add_option( '', '--lastz_seqs_file_dir', dest='lastz_seqs_file_dir', help='Directory of local lastz_seqs.loc file' )
+
+ ( options, args ) = parser.parse_args()
+ if options.ref_name != 'None':
+ ref_name = '[nickname=%s]' % options.ref_name
+ else:
+ ref_name = ''
+ if options.ref_source == 'history':
+ # Reference is a fasta dataset from the history
+ try:
+ # Ensure there is at least 1 sequence in the dataset ( this may not be necessary ).
+ error_msg = "The reference dataset is missing metadata, click the pencil icon in the history item and 'auto-detect' the metadata attributes."
+ ref_sequences = int( options.ref_sequences )
+ if ref_sequences < 1:
+ stop_err( error_msg )
+ except:
+ stop_err( error_msg )
+ else:
+ ref_sequences = 0
+ tmp_w12_name = get_tmp_file_name( suffix='vs_linker.W12' )
+ tmp_T1_name = get_tmp_file_name( suffix='vs_linker.T1' )
+ # Run lastz twice ( with different options ) on the linker sequence and paired end reads,
+ # looking for the linker ( each run finds some the other doesn't )
+ command = 'lastz %s %s W=12 --notrans --exact=18 --match=1,3 O=1 E=3 Y=10 L=18 --ambiguousn --coverage=85 --format=general-:name2,zstart2+,length2,size2 > %s' % \
+ ( options.input3, options.input2, tmp_w12_name )
+ run_command( command )
+ command = 'lastz %s %s T=1 --match=1,2 O=1 E=2 X=15 K=10 Y=15 L=18 --ambiguousn --coverage=85 --format=general-:name2,zstart2+,length2,size2 > %s' % \
+ ( options.input3, options.input2, tmp_T1_name )
+ run_command( command )
+ # Combine the alignment output from the two lastz runs
+ tmp_combined_linker_file_name = get_tmp_file_name( suffix='vs_linker' )
+ command = 'cat %s %s | sort -u > %s' % ( tmp_w12_name, tmp_T1_name, tmp_combined_linker_file_name )
+ run_command( command )
+ # Use the alignment info to split reads into left and right mates
+ tmp_mates_mapping_file_name, tmp_mates_file_name, tmp_mates_short_file_name, tmp_mates_long_file_name = split_paired_reads( options.input2, tmp_combined_linker_file_name )
+ # Align mates to the reference - tmp_align_file_names is a list of file names created by align_mates()
+ tmp_align_file_name_list = align_mates( options.input1, options.ref_source, ref_name, ref_sequences, tmp_mates_short_file_name, tmp_mates_long_file_name )
+ # Combine and convert mate coordinates back to read coordinates
+ paired_mate_unmapper( options.input2, options.input4, tmp_mates_mapping_file_name, tmp_align_file_name_list, options.output )
+ # Delete all temporary files
+ for file_name in tmp_file_names:
+ os.remove( file_name )
+
+if __name__=="__main__": __main__()
diff -r 765c454bcaa7 -r bb7c2b314e3e tools/sr_mapping/lastz_paired_reads_wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/sr_mapping/lastz_paired_reads_wrapper.xml Tue Mar 02 16:40:40 2010 -0500
@@ -0,0 +1,371 @@
+<tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.0.0">
+ <description> map short paired reads against reference sequence</description>
+ <command interpreter="python">lastz_paired_reads_wrapper.py
+#if $seq_name.how_to_name=="yes":
+--ref_name=$seq_name.ref_name
+#else:
+--ref_name="None"
+#end if
+--ref_source=$source.ref_source --input2=$input2 --input3=$input3 --input4=$input4
+#if $source.ref_source=="history":
+--input1=$source.input1
+--ref_sequences=$input1.metadata.sequences
+#else:
+--input1=$source.input1_2bit
+--ref_sequences="None"
+#end if
+--output=$output1 --lastz_seqs_file_dir=${GALAXY_DATA_INDEX_DIR}
+ </command>
+ <inputs>
+ <param name="input2" format="fasta" type="data" label="Align sequencing reads in" />
+ <conditional name="source">
+ <param name="ref_source" type="select" label="Against reference sequences that are">
+ <option value="cached">locally cached</option>
+ <option value="history">in your history</option>
+ </param>
+ <when value="cached">
+ <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+ <options from_file="lastz_seqs.loc">
+ <column name="value" index="1" />
+ <column name="name" index="0" />
+ </options>
+ </param>
+ </when>
+ <when value="history">
+ <param name="input1" type="data" format="fasta" label="Select a reference dataset" />
+ </when>
+ </conditional>
+ <param name="input3" format="fasta" type="data" label="Linker file" />
+ <param name="input4" format="qual454" type="data" label="Select a base quality score 454 dataset" />
+ <conditional name="seq_name">
+ <param name="how_to_name" type="select" label="Do you want to modify reference name?">
+ <option value="no">No</option>
+ <option value="yes">Yes</option>
+ </param>
+ <when value="yes">
+ <param name="ref_name" type="text" size="25" value="Type sequence name here" label="Enter name for the Reference sequence"/>
+ </when>
+ <when value="no" />
+ </conditional>
+ </inputs>
+ <outputs>
+ <data format="sam" name="output1" />
+ </outputs>
+ <requirements>
+ <requirement type="binary">lastz</requirement>
+ </requirements>
+ <tests>
+ <test>
+ <!--
+ input1: a reference genome ( 2bit or fasta )
+ input2: a collection of 454 paired end reads ( a fasta file )
+ input3: a linker sequence ( a very small fasta file )
+ input4: a base quality score 454 file ( qual454 )
+ -->
+ <param name="input2" value="lastz_paired_input2.fasta" ftype="fasta" />
+ <param name="ref_source" value="cached" />
+ <param name="input1_2bit" value="hg18Chr21" />
+ <param name="input3" value="lastz_paired_input3.fasta" ftype="fasta" />
+ <param name="input4" value="lastz_paired_input4.qual454" ftype="qual454" />
+ <param name="how_to_name" value="no" />
+ <output name="output1" file="lastz_paired_out1.sam" />
+ </test>
+ </tests>
+ <help>
+
+**What it does**
+
+**LASTZ** is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. Special scoring sets were derived to improve runtime performance and quality. The Galaxy version of LASTZ is geared towards aligning of short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence. There is excellent, extensive `documentation`__ on LASTZ available, although it hasn't been updated for the version of LASTZ that Galaxy is running (the key changes have to do with output formats, so it is still extremely helpful).
+
+ .. __: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.01.50/README.lastz-1.0…
+
+------
+
+**Input formats**
+
+LASTZ accepts reference and reads in FASTA format. However, because Galaxy supports implicit format conversion the tool will recognize fastq and other method specific formats.
+
+------
+
+**Outputs**
+
+LASTZ generates one output. Depending on the choice you make in *Select output format* drop-down LASTZ will produce a SAM file showing sequence alignments, a list of differences between the reads and reference (Polymorphisms), or a general table with one line per alignment block (Tabular). Examples of these outputs are shown below.
+
+**SAM output**
+
+SAM has 12 columns::
+
+ 1 2 3 4 5 6 7 8 9 10 11 12
+ ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+ HWI-EAS91_1_30788AAXX:1:2:1670:915 99 chr9 58119878 60 36M = 58120234 392 GACCCCTACCCCACCGTGCTCTGGATCTCAGTGTTT IIIIIIIIIIIIIIIIEIIIIIII7IIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
+ HWI-EAS91_1_30788AAXX:1:2:1670:915 147 chr9 58120234 60 36M = 58119878 -392 ATGAGTCGAATTCTATTTTCCAAACTGTTAACAAAA IFIIDI;IIICIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
+
+
+where::
+
+ Column Description
+ --------- ---------------------------------------------------------------------
+ 1. QNAME Query (pair) NAME
+ 2. FLAG bitwise FLAG
+ 3. RNAME Reference sequence NAME
+ 4. POS 1-based leftmost POSition/coordinate of clipped sequence
+ 5. MAPQ MAPping Quality (Phred-scaled)
+ 6. CIGAR extended CIGAR string
+ 7. MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
+ 8. MPOS 1-based Mate POSition
+ 9. ISIZE Inferred insert SIZE
+ 10. SEQ query SEQuence on the same strand as the reference
+ 11. QUAL query QUALity (ASCII-33 gives the Phred base quality)
+ 12. OPT variable OPTional fields in the format TAG:VTYPE:VALUE, tab-separated
+
+The flags are as follows::
+
+ Flag Description
+ ------ -------------------------------------
+ 0x0001 the read is paired in sequencing
+ 0x0002 the read is mapped in a proper pair
+ 0x0004 the query sequence itself is unmapped
+ 0x0008 the mate is unmapped
+ 0x0010 strand of the query (1 for reverse)
+ 0x0020 strand of the mate
+ 0x0040 the read is the first read in a pair
+ 0x0080 the read is the second read in a pair
+ 0x0100 the alignment is not primary
+
+**Polymorphism (SNP or differences) output**
+
+Polymorphism output contains 14 columns::
+
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14
+ --------------------------------------------------------------------------------------------------------------------------------------------------------------
+ chrM 2490 2491 + 5386 HWI-EAS91_1_306UPAAXX:6:1:486:822 10 11 - 36 C A ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC
+ chrM 2173 2174 + 5386 HWI-EAS91_1_306UPAAXX:6:1:259:1389 26 27 + 36 G T GCGTACTTATTCGCCACCATGATTATGACCAGTGTT GCGTACTTATTCGCCACCATGATTATTACCAGTGTT
+
+where::
+
+ 1. (chrM) - Reference sequence id
+ 2. (2490) - Start position of the difference in the reference
+ 3. (2491) - End position of the difference in the reference
+ 4. (+) - Strand of the reference (always plus)
+ 5. (5386) - Length of the reference sequence
+ 6. (HWI...) - read id
+ 7. (10) - Start position of the difference in the read
+ 8. (11) - End position of the difference in the read
+ 9. (+) - Strand of the read
+ 10. (36) - Length of the read
+ 11. (C) - Nucleotide in the reference
+ 12. (A) - Nucleotide in the read
+ 13. (ACC...) - Reference side os the alignment
+ 14. (ACC...) - Read side of the alignment
+
+**Tabular output**
+
+Tabular output is a tab-separated format with 30 columns::
+
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
+ -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+ 14 PHIX174 + 5386 4648 4647 4661 14 ATTTTCGTGATATT EYKX4VC01BV8HS + 204 154 153 167 154 153 167 14 ATTTTCGTGATATT .............. 14M 14/14 100.0% 14/204 6.9% 0/14 0.0% 4494 NA
+ 16 PHIX174 + 5386 3363 3362 3378 16 GACGCCGGATTTGAGA EYKX4VC01AWJ88 - 259 36 35 51 209 208 224 16 GACGCCGGATTTGAGA ................ 16M 16/16 100.0% 16/259 6.2% 0/16 0.0% 3327 NA
+
+The following columns are present::
+
+ Field Meaning
+ ---------------- -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+ 1. score Score of the alignment block. The scale and meaning of this number will vary, depending on the final stage performed and other command-line options.
+ 2. name1 Name of the target sequence.
+ 3. strand1 Target sequence strand, either "+" or "−".
+ 4. size1 Size of the entire target sequence.
+ 5. start1 Starting position of the alignment block in the target, origin-one.
+ 6. zstart1 Starting position of the alignment block in the target, origin-zero.
+ 7. end1 Ending position of the alignment block in the target, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems).
+ 8. length1 Length of the alignment block in the target (excluding gaps).
+ 9. text1 Aligned characters in the target, including gap characters.
+ 10. name2 Name of the query sequence.
+ 11. strand2 Query sequence strand, either "+" or "−".
+ 12. size2 Size of the entire query sequence.
+ 13. start2 Starting position of the alignment block in the query, origin-one.
+ 14. zstart2 Starting position of the alignment block in the query, origin-zero.
+ 15. end2 Ending position of the alignment block in the query, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems).
+ 16. start2+ Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-one. Note that if strand2 is "−", then this is the other end of the block from start2.
+ 17. zstart2+ Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-zero. Note that if strand2 is "−", then this is the other end of the block from zstart2.
+ 18. end2+ Ending position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems). Note that if strand2 is "−", then this is the other end of the block from end2.
+ 19. length2 Length of the alignment block in the query (excluding gaps).
+ 20. text2 Aligned characters in the query, including gap characters.
+ 21. diff Differences between what would be written for text1 and text2. Matches are written as . (period), transitions as : (colon), transversions as X, and gaps as - (hyphen).
+ 22. cigar A CIGAR-like representation of the alignment's path through the Dynamic Programming matrix. This is the short representation, without spaces, described in the Ensembl CIGAR specification.
+ 23./24. identity Fraction of aligned bases in the block that are matches (see Identity). This is written as two fields. The first field is a fraction, written as <n>/<d>. The second field contains the same value, computed as a percentage.
+ 25./26. coverage Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (see Coverage). This is written as two fields. The first field is a fraction, written as <n>/<d>. The second field contains the same value, computed as a percentage.
+ 27./28. gaprate Rate of gaps (also called indels) in the alignment block. This is written as two fields. The first field is a fraction, written as <n>/<d>, with the numerator being the number of alignment columns containing gaps and the denominator being the number without gaps. The second field contains the same value, computed as a percentage.
+ 29. diagonal The diagonal of the start of the alignment block in the dynamic programming matrix, expressed as an identifying number start1-start2.
+ 30. shingle A measurement of the shingle overlap between the target and the query. This is intended for the case where both the target and query are relatively short, and their ends are expected to overlap.
+
+-------
+
+**LASTZ Settings**
+
+There are two setting modes: (1) **Commonly used settings** and (2) **Full Parameter List**.
+
+**Commonly used settings**
+
+There are seven modes::
+
+ Illumina-Solexa/AB-SOLiD 95% identity
+ Illumina-Solexa/AB-SOLiD 85% identity
+ Roche-454 98% identity
+ Roche-454 95% identity
+ Roche-454 90% identity
+ Roche-454 85% identity
+ Roche-454 75% identity
+
+when deciding which one to use consider the following: a 36 bp read with two difference will be 34/36 = 94% identical to the reference.
+
+**Full Parameter List**
+
+This modes gives you a fuller control over lastz. The description of these and other parameters is found at the end of this page. Note, that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs(a)bx.psu.edu.
+
+------
+
+**Do you want to modify reference name?**
+
+This option allows you set the name of the reference sequence manually. This is helpful when, for example, you would like to make reference name compatible with the UCSC naming conventions to be able to display your lastz results as a custom track at UCSC Genome Browser.
+
+------
+
+**LASTZ parameter list**
+
+This is an exhaustive list of LASTZ options. Once again, please note that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs(a)bx.psu.edu::
+
+ target[[s..e]][-] spec/file containing target sequence (fasta or nib)
+ [s..e] defines a subrange of the file
+ - indicates reverse-complement
+ (use --help=files for more details)
+ query[[s..e]][-] spec/file containing query sequences (fasta or nib)
+ if absent, queries come from stdin (unless they
+ aren't needed, as for --self or --tableonly)
+ (use --help=files for more details)
+ --self the target sequence is also the query
+ --quantum the query sequence contains quantum DNA
+ --seed=match<length> use a word with no gaps instead of a seed pattern
+ --seed=half<length> use space-free half-weight word instead of seed pattern
+ --match=<reward>[,<penalty>] set the score values for a match (+<reward>)
+ and mismatch (-<penalty>)
+ --[no]trans[ition][=2] allow one or two transitions in a seed hit
+ (by default a transition is allowed)
+ --word=<bits> set max bits for word hash; use this to trade time for
+ memory, eliminating thrashing for heavy seeds
+ (default is 28 bits)
+ --[no]filter=[<T>:]<M> filter half-weight seed hits, requiring at least M
+ matches and allowing no more than T transversions
+ (default is no filtering)
+ --notwins require just one seed hit
+ --twins=[<min>:]<maxgap> require two nearby seed hits on the same diagonal
+ (default is twins aren't required)
+ --notwins allow single, isolated seeds
+ --[no]recoverseeds avoid losing seeds in hash collisions. Cannot be used with --twins
+ --seedqueue=<entries> set number of entries in seed hit queue
+ (default is 262144)
+ --anchors=<file> read anchors from a file, instead of discovering anchors
+ via seeding
+ --recoverhits recover hash-collision seed hits
+ (default is not to recover seed hits)
+ --step=<length> set step length (default is 1)
+ --maxwordcount=<limit> words occurring more often than <limit> in the target
+ are not eligible for seeds
+ --strand=both search both strands
+ --strand=plus search + strand only (matching strand of query spec)
+ --strand=minus search - strand only (opposite strand of query spec)
+ (by default both strands are searched)
+ --ambiguousn treat N as an ambiguous nucleotide
+ (by default N is treated as a sequence splicing character)
+ --[no]gfextend perform gap-free extension of seed hits to HSPs
+ (by default no extension is performed)
+ --[no]chain perform chaining
+ --chain=<diag,anti> perform chaining with given penalties for diagonal and
+ anti-diagonal
+ (by default no chaining is performed)
+ --[no]gapped perform gapped alignment (instead of gap-free)
+ (by default gapped alignment is performed)
+ --score[s]=<file> read substitution scores from a file
+ (default is HOXD70)
+ --unitscore[s] scores are +1/-1 for match/mismatch
+ --gap=<[open,]extend> set gap open and extend penalties (default is 400,30)
+ --xdrop=<score> set x-drop threshold (default is 10*sub[A][A])
+ --ydrop=<score> set y-drop threshold (default is open+300extend)
+ --infer[=<control>] infer scores from the sequences, then use them
+ --inferonly[=<control>] infer scores, but don't use them (requires --infscores)
+ all inference options are read from the control file
+ --infscores[=<file>] write inferred scores to a file
+ --hspthresh=<score> set threshold for high scoring pairs (default is 3000)
+ ungapped extensions scoring lower are discarded
+ <score> can also be a percentage or base count
+ --entropy adjust for entropy when qualifying HSPs in the x-drop extension
+ method
+ --noentropy don't adjust for entropy when qualifying HSPs
+ --exact=<length> set threshold for exact matches
+ if specified, exact matches are found rather than high
+ scoring pairs (replaces --hspthresh)
+ --inner=<score> set threshold for HSPs during interpolation
+ (default is no interpolation)
+ --gappedthresh=<score> set threshold for gapped alignments
+ gapped extensions scoring lower are discarded
+ <score> can also be a percentage or base count
+ (default is to use same value as --hspthresh)
+ --ball=<score> set minimum score required of words 'in' a quantum ball
+ --[no]entropy involve entropy in filtering high scoring pairs
+ (default is "entropy")
+ --[no]mirror report/use mirror image of all gap-free alignments
+ (default is "mirror" for self-alignments only)
+ --traceback=<bytes> space for trace-back information
+ (default is 80.0M)
+ --masking=<count> mask any position in target hit this many times
+ zero indicates no masking
+ (default is no masking)
+ --targetcapsule=<capsule_file> the target seed word position table and seed
+ (as well as the target sequence)are read from specified file
+ --segments=<segment_file> read segments from a file, instead of discovering
+ them via seeding. Replaces other seeding or gap-free extension
+ options
+ --[no]census[=<file>] count/report how many times each target base aligns
+ (default is to not report census)
+ --identity=<min>[..<max>] filter alignments by percent identity
+ 0<=min<=max<=100; blocks (or HSPs) outside min..max
+ are discarded
+ (default is no identity filtering)
+ --coverage=<min>[..<max>] filter alignments by percentage pf query covered
+ 0<=min<=max<=100; blocks (or HSPs) outside min..max
+ are discarded
+ (default is no query coverage filtering)
+ --notrivial do not output trivial self-alignment block if the target and query
+ sequences are identical. Using --self enables this option automatically
+ --output=<output_file> write the alignments to the specified file name instead of stdout
+ --code=<file> give quantum code for query sequence (only for display)
+ --format=<type> specify output format; one of lav, axt, maf, maf+, maf-, text,
+ lav+text, cigar, text, rdplot, general, or general:<fields>
+ (by default output is LAV)
+ --rdotplot=<file> create an additional output file suitable for plotting the alignments
+ with the R statistical package.
+ --markend Just before normal completion, write "# lastz end-of-file" to output file
+ --census[=<output_file>] count and report how many times each target base aligns, up
+ to 255. Ns are included in the count
+ --census16[=<output_file>] count and report how many times each target base aligns, up
+ up 65 thousand
+ --census32[=<output_file>] count and report how many times each target bas aligns, up
+ to 4 billion
+ --writecapsule=<capsule_file> just write out a targegt capsule file and quit; don't
+ search for seeds or perform subsequent stages
+ --verbosity=<level> set info level (0 is minimum, 10 is everything)
+ (default is 0)
+ --[no]runtime report runtime in the output file
+ (default is to not report runtime)
+ --tableonly[=count] just produce the target position table, don't
+ search for seeds
+ --[no]stats[=<file>] show search statistics (or don't)
+ (not available in this build)
+ --version report the program version and quit
+ --help list all options
+ --help=files list information about file specifiers
+ --help=short[cuts] list blastz-compatible shortcuts
+ --help=yasra list yasra-specific shortcuts
+
+ </help>
+</tool>
diff -r 765c454bcaa7 -r bb7c2b314e3e tools/sr_mapping/lastz_wrapper.xml
--- a/tools/sr_mapping/lastz_wrapper.xml Tue Mar 02 16:35:21 2010 -0500
+++ b/tools/sr_mapping/lastz_wrapper.xml Tue Mar 02 16:40:40 2010 -0500
@@ -24,8 +24,8 @@
<inputs>
<param name="input2" format="fasta" type="data" label="Align sequencing reads in" />
<conditional name="source">
- <param name="ref_source" type="select" label="Against reference sequences">
- <option value="cached">that are locally cached</option>
+ <param name="ref_source" type="select" label="Against reference sequences that are">
+ <option value="cached">locally cached</option>
<option value="history">in your history</option>
</param>
<when value="cached">
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/765c454bcaa7
changeset: 3467:765c454bcaa7
user: Anton Nekrutenko <anton(a)bx.psu.edu>
date: Tue Mar 02 16:35:21 2010 -0500
description:
Modifications to pileup_parser
diffstat:
static/images/pileup_parser_help1.png | 0
static/images/pileup_parser_help2.png | 0
static/images/pileup_parser_help3.png | 0
static/images/pileup_parser_help4.png | 0
test-data/pileup_parser.10col.20-3-yes-yes-yes-no.pileup.out | 86 ++++++
test-data/pileup_parser.10col.20-3-yes-yes-yes-yes.pileup.out | 86 ++++++
tools/samtools/pileup_parser.pl | 22 +-
tools/samtools/pileup_parser.xml | 128 ++++++++-
8 files changed, 307 insertions(+), 15 deletions(-)
diffs (526 lines):
diff -r 1d11aec88053 -r 765c454bcaa7 static/images/pileup_parser_help1.png
Binary file static/images/pileup_parser_help1.png has changed
diff -r 1d11aec88053 -r 765c454bcaa7 static/images/pileup_parser_help2.png
Binary file static/images/pileup_parser_help2.png has changed
diff -r 1d11aec88053 -r 765c454bcaa7 static/images/pileup_parser_help3.png
Binary file static/images/pileup_parser_help3.png has changed
diff -r 1d11aec88053 -r 765c454bcaa7 static/images/pileup_parser_help4.png
Binary file static/images/pileup_parser_help4.png has changed
diff -r 1d11aec88053 -r 765c454bcaa7 test-data/pileup_parser.10col.20-3-yes-yes-yes-no.pileup.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_parser.10col.20-3-yes-yes-yes-no.pileup.out Tue Mar 02 16:35:21 2010 -0500
@@ -0,0 +1,86 @@
+chrM 13 14 A A 56 0 25 18 16 0 1 0 17 1
+chrM 18 19 T T 55 0 25 20 0 0 1 18 19 1
+chrM 35 36 A A 103 0 25 30 27 0 1 0 28 1
+chrM 58 59 A A 50 0 24 16 12 1 0 0 13 1
+chrM 59 60 C C 50 0 24 16 1 15 0 0 16 1
+chrM 157 158 A G 117 117 19 62 0 0 56 0 56 56
+chrM 170 171 T T 141 0 21 46 0 0 1 45 46 1
+chrM 172 173 A A 130 0 20 42 36 1 0 0 37 1
+chrM 173 174 A A 122 0 21 40 38 1 0 0 39 1
+chrM 187 188 A A 36 0 21 13 11 0 1 0 12 1
+chrM 195 196 T T 17 0 19 5 0 0 1 4 5 1
+chrM 284 285 G G 34 0 15 11 0 0 10 1 11 1
+chrM 285 286 T T 33 0 15 11 1 0 0 7 8 1
+chrM 303 304 G G 41 0 18 13 1 0 11 0 12 1
+chrM 310 311 T T 41 0 18 13 0 1 0 11 12 1
+chrM 347 348 T T 4 0 20 3 1 0 0 2 3 1
+chrM 354 355 A C 14 36 25 4 1 3 0 0 4 3
+chrM 355 356 T C 39 39 25 4 0 4 0 0 4 4
+chrM 380 381 C T 77 108 25 28 0 0 0 24 24 24
+chrM 383 384 A A 76 0 25 30 25 1 0 0 26 1
+chrM 385 386 A G 88 120 25 32 0 0 29 0 29 29
+chrM 414 415 C T 75 75 25 16 0 0 0 15 15 15
+chrM 464 465 C C 169 0 25 65 1 58 0 0 59 1
+chrM 468 469 T T 207 0 25 66 0 0 1 56 57 1
+chrM 471 472 C C 187 0 25 72 1 64 0 0 65 1
+chrM 490 491 C C 212 0 23 79 0 73 0 1 74 1
+chrM 506 507 A A 150 0 21 76 64 1 0 0 65 1
+chrM 510 511 C C 213 0 21 72 1 68 0 0 69 1
+chrM 526 527 A A 164 0 22 58 51 1 0 0 52 1
+chrM 527 528 A A 164 0 22 58 48 0 1 0 49 1
+chrM 536 537 A A 138 0 23 49 42 1 0 0 43 1
+chrM 557 558 T T 83 0 23 27 0 0 1 23 24 1
+chrM 606 607 G G 105 0 24 43 0 0 33 2 35 2
+chrM 618 619 T T 117 0 24 48 0 1 0 34 35 1
+chrM 627 628 G G 108 0 22 57 1 0 51 0 52 1
+chrM 659 660 C C 166 0 19 58 1 53 0 0 54 1
+chrM 668 669 C C 135 0 19 42 1 40 1 0 42 2
+chrM 713 714 A A 127 0 23 96 90 1 0 0 91 1
+chrM 719 720 T T 130 0 24 96 0 0 1 77 78 1
+chrM 736 737 A A 98 0 24 98 87 1 0 0 88 1
+chrM 747 748 A A 97 0 25 86 80 1 0 0 81 1
+chrM 749 750 A A 93 0 25 77 71 2 0 0 73 2
+chrM 759 760 T T 106 0 25 86 0 0 1 69 70 1
+chrM 762 763 A A 99 0 25 83 76 1 0 0 77 1
+chrM 763 764 G G 107 0 25 86 1 0 75 0 76 1
+chrM 764 765 G G 88 0 25 77 0 0 68 1 69 1
+chrM 767 768 T T 102 0 25 71 1 0 0 65 66 1
+chrM 777 778 G G 108 0 25 63 0 0 58 1 59 1
+chrM 784 785 A A 99 0 25 63 51 1 0 0 52 1
+chrM 790 791 G G 155 0 25 60 0 0 55 1 56 1
+chrM 794 795 T T 212 0 25 74 1 0 0 62 63 1
+chrM 807 808 C C 226 0 22 132 1 110 0 0 111 1
+chrM 808 809 T T 242 0 22 134 0 1 0 109 110 1
+chrM 809 810 A A 243 0 22 144 128 0 1 0 129 1
+chrM 814 815 C C 246 0 22 160 1 142 0 0 143 1
+chrM 815 816 A A 255 0 22 169 159 0 1 0 160 1
+chrM 816 817 A A 254 0 22 171 150 1 0 0 151 1
+chrM 819 820 A A 255 0 22 183 157 0 0 1 158 1
+chrM 822 823 T T 252 0 22 192 0 1 0 171 172 1
+chrM 825 826 A A 255 0 22 198 177 0 1 0 178 1
+chrM 829 830 G G 255 0 22 198 1 0 185 0 186 1
+chrM 837 838 G G 255 0 22 169 0 0 160 1 161 1
+chrM 841 842 C C 239 0 22 173 1 156 0 0 157 1
+chrM 856 857 C C 254 0 23 124 1 114 0 0 115 1
+chrM 858 859 A A 250 0 23 118 110 0 1 0 111 1
+chrM 859 860 A A 255 0 23 115 101 1 0 0 102 1
+chrM 864 865 G G 255 0 23 115 1 0 109 0 110 1
+chrM 866 867 A A 224 0 23 105 81 1 0 0 82 1
+chrM 872 873 C C 206 0 23 94 1 84 0 0 85 1
+chrM 873 874 A A 208 0 23 94 80 1 0 0 81 1
+chrM 931 932 C C 53 0 23 22 2 18 0 0 20 2
+chrM 936 937 C C 98 0 24 31 1 21 0 0 22 1
+chrM 950 951 C C 191 0 23 76 1 61 0 0 62 1
+chrM 951 952 A A 223 0 24 81 78 2 0 0 80 2
+chrM 952 953 C C 179 0 24 86 2 67 0 0 69 2
+chrM 956 957 T T 237 0 23 110 0 0 1 91 92 1
+chrM 957 958 C C 251 0 23 117 1 96 0 0 97 1
+chrM 966 967 A A 246 0 23 125 119 1 0 0 120 1
+chrM 974 975 C C 255 0 23 125 1 111 1 0 113 2
+chrM 980 981 C C 247 0 23 123 0 111 1 0 112 1
+chrM 981 982 C C 255 0 23 122 2 106 0 0 108 2
+chrM 982 983 C C 252 0 23 122 1 105 0 0 106 1
+chrM 983 984 A A 250 0 23 119 105 1 0 0 106 1
+chrM 987 988 A A 243 0 23 94 79 1 0 0 80 1
+chrM 1005 1006 C C 138 0 18 49 1 43 0 0 44 1
+chrM 1025 1026 G G 19 0 8 33 0 0 31 1 32 1
diff -r 1d11aec88053 -r 765c454bcaa7 test-data/pileup_parser.10col.20-3-yes-yes-yes-yes.pileup.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_parser.10col.20-3-yes-yes-yes-yes.pileup.out Tue Mar 02 16:35:21 2010 -0500
@@ -0,0 +1,86 @@
+chrM 13 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII 16 0 1 0 17 1
+chrM 18 19 T T 55 0 25 20 ..................GG IIIIIIIIIIIIIIIIII'A 0 0 1 18 19 1
+chrM 35 36 A A 103 0 25 30 .$..N...G.....C...............^:. 7:>"EIIIEI5><$C7B?B=IIIIIIIIII 27 0 1 0 28 1
+chrM 58 59 A A 50 0 24 16 ...............C IB20III:<DIII#II 12 1 0 0 13 1
+chrM 59 60 C C 50 0 24 16 .$.............A. I?>=IIIIIIIIIIBI 1 15 0 0 16 1
+chrM 157 158 A G 117 117 19 62 GGGGGGGGGGGGGGGGGGGNNNGGGGGG.GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGg^:g II6IIII<4I+IIIIIIII"""IIIIII$IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII> 0 0 56 0 56 56
+chrM 170 171 T T 141 0 21 46 .$.$.$.$.$.....................................,,.^:G IIIII=>IIIIIIIIIIIIIIDDII7IGIIIIIHIIIIIIIIIBI8 0 0 1 45 46 1
+chrM 172 173 A A 130 0 20 42 .$.$...C...............................,,... 914HG841?IA0III:IB@>;@FIIIIIIIEIIBII;IIIII 36 1 0 0 37 1
+chrM 173 174 A A 122 0 21 40 .$.$..........C......................,,... ?DCI?@I7C5I*I9C9IIIE?C>::I8IIIIIIIIIIIII 38 1 0 0 39 1
+chrM 187 188 A A 36 0 21 13 G$.$.$....,,.... II5II5,IIIIII 11 0 1 0 12 1
+chrM 195 196 T T 17 0 19 5 G.... <IIII 0 0 1 4 5 1
+chrM 284 285 G G 34 0 15 11 ....T....^!.^!. IIIIIIIIIII 0 0 10 1 11 1
+chrM 285 286 T T 33 0 15 11 ..C..N.A... AI&II"II(II 1 0 0 7 8 1
+chrM 303 304 G G 41 0 18 13 ...A....,.,., IIIIIIIIIIII* 1 0 11 0 12 1
+chrM 310 311 T T 41 0 18 13 .$...C...,.,., IIIIIIIIIIII* 0 1 0 11 12 1
+chrM 347 348 T T 4 0 20 3 ,$.$A IIA 1 0 0 2 3 1
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diff -r 1d11aec88053 -r 765c454bcaa7 tools/samtools/pileup_parser.pl
--- a/tools/samtools/pileup_parser.pl Tue Mar 02 13:20:47 2010 -0500
+++ b/tools/samtools/pileup_parser.pl Tue Mar 02 16:35:21 2010 -0500
@@ -4,7 +4,7 @@
use POSIX;
-die "Usage: pileup_parser.pl <in_file> <ref_base_column> <read_bases_column> <base_quality_column> <coverage column> <qv cutoff> <coverage cutoff> <SNPs only?> <output bed?> <coord_column> <out_file>\n" unless @ARGV == 11;
+die "Usage: pileup_parser.pl <in_file> <ref_base_column> <read_bases_column> <base_quality_column> <coverage column> <qv cutoff> <coverage cutoff> <SNPs only?> <output bed?> <coord_column> <out_file> <total_diff> <print_qual_bases>\n" unless @ARGV == 13;
my $in_file = $ARGV[0];
my $ref_base_column = $ARGV[1]-1; # 1 based
@@ -17,6 +17,8 @@
my $bed = $ARGV[8]; #set to "Yes" to convert coordinates to bed format (0-based start, 1-based end); set to "No" to leave as is
my $coord_column = $ARGV[9]-1; #1 based
my $out_file = $ARGV[10];
+my $total_diff = $ARGV[11]; # set to "Yes" to print total number of deviant based
+my $print_qual_bases = $ARGV[12]; #set to "Yes" to print quality and read base columns
my $invalid_line_counter = 0;
my $first_skipped_line = "";
@@ -24,6 +26,7 @@
my $above_qv_bases = 0;
my $SNPs_exist = 0;
my $out_string = "";
+my $diff_count = 0;
open (IN, "<$in_file") or die "Cannot open $in_file $!\n";
open (OUT, ">$out_file") or die "Cannot open $out_file $!\n";
@@ -65,6 +68,7 @@
{
$SNPs_exist = 1;
$SNPs{ uc( $bases[ $base ] ) } += 1;
+ $diff_count += 1;
} elsif ( $bases[ $base ] =~ m/[\.,]/ ) {
$SNPs{ uc( $fields[ $ref_base_column ] ) } += 1;
}
@@ -77,11 +81,24 @@
$fields[ $coord_column ] = "$start\t$end";
}
+ if ($print_qual_bases ne "Yes") {
+ $fields[ $base_quality_column ] = "";
+ $fields[ $read_bases_column ] = "";
+ }
+
+
$out_string = join("\t", @fields); # \t$read_bases\t$base_quality";
foreach my $SNP (sort keys %SNPs) {
$out_string .= "\t$SNPs{$SNP}";
}
- $out_string .= "\t$above_qv_bases\n";
+
+ if ($total_diff eq "Yes") {
+ $out_string .= "\t$above_qv_bases\t$diff_count\n";
+ } else {
+ $out_string .= "\t$above_qv_bases\n";
+ }
+
+ $out_string =~ s/\t+/\t/g;
if ( $SNPs_only eq "Yes" ) {
print OUT $out_string if $SNPs_exist == 1;
@@ -94,6 +111,7 @@
%SNPs = ('A',0,'T',0,'C',0,'G',0);
$above_qv_bases = 0;
$SNPs_exist = 0;
+ $diff_count = 0;
}
diff -r 1d11aec88053 -r 765c454bcaa7 tools/samtools/pileup_parser.xml
--- a/tools/samtools/pileup_parser.xml Tue Mar 02 13:20:47 2010 -0500
+++ b/tools/samtools/pileup_parser.xml Tue Mar 02 16:35:21 2010 -0500
@@ -1,9 +1,9 @@
-<tool id="pileup_parser" name="Filter pileup" version="1.0.1">>
+<tool id="pileup_parser" name="Filter pileup" version="1.0.2">>
<description>on coverage and SNPs</description>
<command interpreter="perl">
- #if $pileup_type.type_select == "six" #pileup_parser.pl $input "3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1
- #elif $pileup_type.type_select == "ten" #pileup_parser.pl $input "3" "9" "10" "8" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1
- #elif $pileup_type.type_select == "manual" #pileup_parser.pl $input $pileup_type.ref_base_column $pileup_type.read_bases_column $pileup_type.read_qv_column $pileup_type.cvrg_column $qv_cutoff $cvrg_cutoff $snps_only $interval $pileup_type.coord_column $out_file1
+ #if $pileup_type.type_select == "six" #pileup_parser.pl $input "3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 $diff $qc_base
+ #elif $pileup_type.type_select == "ten" #pileup_parser.pl $input "3" "9" "10" "8" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 $diff $qc_base
+ #elif $pileup_type.type_select == "manual" #pileup_parser.pl $input $pileup_type.ref_base_column $pileup_type.read_bases_column $pileup_type.read_qv_column $pileup_type.cvrg_column $qv_cutoff $cvrg_cutoff $snps_only $interval $pileup_type.coord_column $out_file1 $diff $qc_base
#end if#
</command>
<inputs>
@@ -36,6 +36,14 @@
<option value="No" selected="true">No</option>
<option value="Yes">Yes</option>
</param>
+ <param name="diff" label="Print total number of differences?" type="select" help="See "Example 3" below for explanation">
+ <option value="No" selected="true">No</option>
+ <option value="Yes">Yes</option>
+ </param>
+ <param name="qc_base" label="Print quality and base string?" type="select" help="See "Example 4" below for explanation">
+ <option value="No">No</option>
+ <option value="Yes" selected="true">Yes</option>
+ </param>
</inputs>
<outputs>
@@ -54,6 +62,8 @@
<param name="cvrg_cutoff" value="3" />
<param name="snps_only" value="Yes"/>
<param name="interval" value="Yes" />
+ <param name="diff" value="No" />
+ <param name="qc_base" value="Yes" />
</test>
<test>
<param name="input" value="pileup_parser.6col.pileup"/>
@@ -63,6 +73,8 @@
<param name="cvrg_cutoff" value="3" />
<param name="snps_only" value="Yes"/>
<param name="interval" value="No" />
+ <param name="diff" value="No" />
+ <param name="qc_base" value="Yes" />
</test>
<test>
<param name="input" value="pileup_parser.6col.pileup"/>
@@ -72,6 +84,8 @@
<param name="cvrg_cutoff" value="3" />
<param name="snps_only" value="No"/>
<param name="interval" value="No" />
+ <param name="diff" value="No" />
+ <param name="qc_base" value="Yes" />
</test>
<test>
<param name="input" value="pileup_parser.10col.pileup"/>
@@ -81,6 +95,8 @@
<param name="cvrg_cutoff" value="3" />
<param name="snps_only" value="Yes"/>
<param name="interval" value="Yes" />
+ <param name="diff" value="No" />
+ <param name="qc_base" value="Yes" />
</test>
<test>
<param name="input" value="pileup_parser.10col.pileup"/>
@@ -95,7 +111,43 @@
<param name="cvrg_cutoff" value="3" />
<param name="snps_only" value="Yes"/>
<param name="interval" value="Yes" />
+ <param name="diff" value="No" />
+ <param name="qc_base" value="Yes" />
</test>
+ <test>
+ <param name="input" value="pileup_parser.10col.pileup"/>
+ <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes-yes-yes.pileup.out"/>
+ <param name="type_select" value="manual"/>
+ <param name="ref_base_column" value="3"/>
+ <param name="read_bases_column" value="9"/>
+ <param name="read_qv_column" value="10"/>
+ <param name="cvrg_column" value="8"/>
+ <param name="coord_column" value="2"/>
+ <param name="qv_cutoff" value="20" />
+ <param name="cvrg_cutoff" value="3" />
+ <param name="snps_only" value="Yes"/>
+ <param name="interval" value="Yes" />
+ <param name="diff" value="Yes" />
+ <param name="qc_base" value="Yes" />
+ </test>
+ <test>
+ <param name="input" value="pileup_parser.10col.pileup"/>
+ <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes-yes-no.pileup.out"/>
+ <param name="type_select" value="manual"/>
+ <param name="ref_base_column" value="3"/>
+ <param name="read_bases_column" value="9"/>
+ <param name="read_qv_column" value="10"/>
+ <param name="cvrg_column" value="8"/>
+ <param name="coord_column" value="2"/>
+ <param name="qv_cutoff" value="20" />
+ <param name="cvrg_cutoff" value="3" />
+ <param name="snps_only" value="Yes"/>
+ <param name="interval" value="Yes" />
+ <param name="diff" value="Yes" />
+ <param name="qc_base" value="No" />
+ </test>
+
+
</tests>
<help>
@@ -120,7 +172,7 @@
---------------------------------
chrM 412 A 2 ., II
chrM 413 G 4 ..t, IIIH
- chrM 414 C 4 ...a III2
+ chrM 414 C 4 ..Ta III2
chrM 415 C 4 TTTt III7
where::
@@ -143,7 +195,7 @@
------------------------------------------------
chrM 412 A A 75 0 25 2 ., II
chrM 413 G G 72 0 25 4 ..t, IIIH
- chrM 414 C C 75 0 25 4 ...a III2
+ chrM 414 C C 75 0 25 4 ..Ta III2
chrM 415 C T 75 75 25 4 TTTt III7
where::
@@ -178,18 +230,21 @@
- Number of **T** variants
- Number of read bases covering this position, where quality is equal to or higher than the value set by **Do not consider read bases with quality lower than** option.
+Optionally, if **Print total number of differences?** is set to **Yes**, the tool will append the sixth column with the total number of deviants (see below).
+
2. If **Convert coordinates to intervals?** is set to **Yes**, the tool replaces the position column (typically the second column) with a pair of tab-delimited start/end values.
For example, if you are calling variants with base quality above 20 on this dataset::
chrM 412 A 2 ., II
chrM 413 G 4 ..t, III2
- chrM 414 C 4 ...a III2
+ chrM 414 C 4 ..Ta III2
chrM 415 C 4 TTTt III7
you will get::
chrM 413 G 4 ..t, IIIH 0 0 2 1 3
+ chrM 414 C 4 ..Ta III2 1 1 0 1 3
chrM 415 C 4 TTTt III7 0 0 0 4 4
where::
@@ -200,18 +255,29 @@
2 Position (1-based)
3 Reference base at that position
4 Coverage (# reads aligning over that position)
- 5 Bases within reads where (see Galaxy wiki for more info)
+ 5 Bases within reads where (see Galaxy wiki for more info)
6 Quality values (phred33 scale, see Galaxy wiki for more)
7 Number of A variants
8 Number of C variants
9 Number of G variants
10 Number of T variants
11 Quality adjusted coverage:
- Number of read bases (i.e., # of reads) with quality above the set threshold
+ 12 Number of read bases (i.e., # of reads) with quality above the set threshold
+ 13 Total number of deviants (if Convert coordinates to intervals? is set to yes)
+
+if **Print total number of differences?** is set to **Yes**, you will get::
+
+ chrM 413 G 4 ..t, IIIH 0 0 2 1 3 1
+ chrM 414 C 4 ..Ta III2 1 2 0 1 3 2
+ chrM 415 C 4 TTTt III7 0 0 0 4 4 0
-and if **Convert coordinates to intervals?** is set to **Yes**, you will get one additional column::
+Note the additional column 13, that contains the number of deviant reads (e.g., there are two deviants, T and a, for position 414).
+
+
+Finally, if **Convert coordinates to intervals?** is set to **Yes**, you will get one additional column with the end coordinate::
chrM 412 413 G 4 ..t, III2 0 0 2 1 3
+ chrM 414 415 C 4 ..Ta III2 1 2 0 1 3
chrM 414 415 C 4 TTTt III7 0 0 0 4 4
where::
@@ -230,13 +296,14 @@
10 Number of G variants
11 Number of T variants
12 Quality adjusted coverage
+ 13 Total number of deviants (if Convert coordinates to intervals? is set to yes)
Note that in this case the coordinates of SNPs were converted to intervals, where the start coordinate is 0-based and the end coordinate in 1-based using the UCSC Table Browser convention.
Although three positions have variants in the original file (413, 414, and 415), only 413 and 415 are reported because the quality values associated with these two SNPs are above the threshold of 20. In the case of 414 the **a** allele has a quality value of 17 ( ord("2")-33 ), and is therefore not reported. Note that five columns have been added to each of the reported lines::
- chrM 413 G 4 ..t, IIIH 0 0 0 1 3
+ chrM 413 G 4 ..t, IIIH 0 0 2 1 3
Here, there is one variant, **t**. Because the fourth column represents **T** counts, it is incremented by 1. The last column shows that at this position, three reads have bases above the quality threshold of 20.
@@ -248,7 +315,7 @@
chrM 412 A 2 ., II
chrM 413 G 4 ..t, III2
- chrM 414 C 4 ...a III2
+ chrM 414 C 4 ..Ta III2
chrM 415 C 4 TTTt III7
To call all variants (with no restriction by coverage) with quality above phred value of 20, we will need to set the parameters as follows:
@@ -258,6 +325,7 @@
Running the tool with these parameters will return::
chrM 413 G 4 ..t, IIIH 0 0 0 1 3
+ chrM 414 C 4 ..Ta III2 0 2 0 1 3
chrM 415 C 4 TTTt III7 0 0 0 4 4
**Note** that position 414 is not reported because the *a* variant has associated quality value of 17 (because ord('2')-33 = 17) and is below the phred threshold of 20 set by the **Count variants with quality above this value** parameter.
@@ -274,12 +342,46 @@
chrM 412 A 2 ., II 2 0 0 0 2
chrM 413 G 4 ..t, III2 0 0 2 1 3
- chrM 414 C 4 ...a III2 3 0 0 0 3
+ chrM 414 C 4 ..Ta III2 0 2 0 1 3
chrM 415 C 4 TTTt III7 0 0 0 4 4
Here, you can see that although the total coverage at position 414 is 4 (column 4), the quality adjusted coverage is 3 (last column). This is because only three out of four reads have bases with quality above the set threshold of 20 (the actual qualities are III2 or, after conversion, 40, 40, 40, 17).
One can use the last column of this dataset to filter out (using Galaxy's **Filter** tool) positions where quality adjusted coverage (last column) is below a set threshold.
+
+------
+
+**Example 3**: Report everything and print total number of differences
+
+If you set the **Print total number of differences?** to **Yes** the tool will print an additional column with the total number of reads where a devinat base is above the quality threshold cutoff. So, seetiing parametrs like this:
+
+.. image:: ../static/images/pileup_parser_help3.png
+
+will produce this::
+
+ chrM 412 A 2 ., II 2 0 0 0 2 0
+ chrM 413 G 4 ..t, III2 0 0 2 1 3 1
+ chrM 414 C 4 ..Ta III2 0 2 0 1 3 1
+ chrM 415 C 4 TTTt III7 0 0 0 4 4 0
+
+
+-----
+
+**Example 4**: Report everything, print total number of differences, and ignore qualities and read bases
+
+Setting **Print quality and base string?** to **Yes** as shown here:
+
+.. image:: ../static/images/pileup_parser_help4.png
+
+will produce this::
+
+ chrM 412 A 2 2 0 0 0 2 0
+ chrM 413 G 4 0 0 2 1 3 1
+ chrM 414 C 4 0 2 0 1 3 1
+ chrM 415 C 4 0 0 0 4 4 0
+
+
+
</help>
</tool>
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/1d11aec88053
changeset: 3466:1d11aec88053
user: Nate Coraor <nate(a)bx.psu.edu>
date: Tue Mar 02 13:20:47 2010 -0500
description:
Fix SGE bug reported in issue #281
diffstat:
lib/galaxy/jobs/runners/sge.py | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diffs (11 lines):
diff -r 0967cea77985 -r 1d11aec88053 lib/galaxy/jobs/runners/sge.py
--- a/lib/galaxy/jobs/runners/sge.py Tue Mar 02 12:32:44 2010 -0500
+++ b/lib/galaxy/jobs/runners/sge.py Tue Mar 02 13:20:47 2010 -0500
@@ -337,6 +337,6 @@
self.queue.put( sge_job_state )
elif job.state == model.Job.states.QUEUED:
log.debug( "(%s/%s) is still in SGE queued state, adding to the SGE queue" % ( job.id, job.job_runner_external_id ) )
- sge_job_state.old_state = DRMAA.Session.QUEUED
+ sge_job_state.old_state = DRMAA.Session.QUEUED_ACTIVE
sge_job_state.running = False
self.queue.put( sge_job_state )
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/0967cea77985
changeset: 3465:0967cea77985
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Tue Mar 02 12:32:44 2010 -0500
description:
Fix comment and indentation.
diffstat:
templates/workflow/display.mako | 6 +++---
1 files changed, 3 insertions(+), 3 deletions(-)
diffs (16 lines):
diff -r 69db124587e3 -r 0967cea77985 templates/workflow/display.mako
--- a/templates/workflow/display.mako Tue Mar 02 12:10:43 2010 -0500
+++ b/templates/workflow/display.mako Tue Mar 02 12:32:44 2010 -0500
@@ -86,9 +86,9 @@
<%def name="render_item( workflow, steps )">
<%
- # HACK: Rendering workflow steps requires that trans have a history; however, if a user's first visit to Galaxy is here, he won't have a history
- # and an error will occur. To prevent this error, make sure user has a history.
- trans.get_history( create=True )
+ # HACK: Rendering workflow steps requires that trans have a history; however, if it's user's first visit to Galaxy is here, he won't have a history
+ # and an error will occur. To prevent this error, make sure user has a history.
+ trans.get_history( create=True )
%>
<table class="annotated-item">
<tr><th>Step</th><th class="annotation">Description/Notes</th></tr>
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/69db124587e3
changeset: 3464:69db124587e3
user: Nate Coraor <nate(a)bx.psu.edu>
date: Tue Mar 02 12:10:43 2010 -0500
description:
I am having a bad day
diffstat:
scripts/scramble/scripts/pbs_python.py | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
diffs (14 lines):
diff -r 5f6b53b08623 -r 69db124587e3 scripts/scramble/scripts/pbs_python.py
--- a/scripts/scramble/scripts/pbs_python.py Tue Mar 02 12:08:01 2010 -0500
+++ b/scripts/scramble/scripts/pbs_python.py Tue Mar 02 12:10:43 2010 -0500
@@ -29,8 +29,8 @@
i = open( 'setup.py.orig', 'r' )
o = open( 'setup.py', 'w' )
for line in i.readlines():
- if line == " version = '2.9.0',\n":
- line = " version = '2.9.4',\n"
+ if line == " version = '2.9.0',\n":
+ line = " version = '2.9.4',\n"
print >>o, line,
i.close()
o.close()
1
0
details: http://www.bx.psu.edu/hg/galaxy/rev/5f6b53b08623
changeset: 3463:5f6b53b08623
user: Nate Coraor <nate(a)bx.psu.edu>
date: Tue Mar 02 12:08:01 2010 -0500
description:
pbs_python 2.9.8 doesn't work
diffstat:
eggs.ini | 2 +-
scripts/scramble/scripts/pbs_python.py | 13 +++++++++++++
2 files changed, 14 insertions(+), 1 deletions(-)
diffs (35 lines):
diff -r db7ee1dc19c4 -r 5f6b53b08623 eggs.ini
--- a/eggs.ini Tue Mar 02 11:52:16 2010 -0500
+++ b/eggs.ini Tue Mar 02 12:08:01 2010 -0500
@@ -16,7 +16,7 @@
Cheetah = 2.2.2
DRMAA_python = 0.2
MySQL_python = 1.2.3c1
-pbs_python = 2.9.8
+pbs_python = 2.9.4
psycopg2 = 2.0.6
pycrypto = 2.0.1
pysam = 0.1.1
diff -r db7ee1dc19c4 -r 5f6b53b08623 scripts/scramble/scripts/pbs_python.py
--- a/scripts/scramble/scripts/pbs_python.py Tue Mar 02 11:52:16 2010 -0500
+++ b/scripts/scramble/scripts/pbs_python.py Tue Mar 02 12:08:01 2010 -0500
@@ -22,6 +22,19 @@
# run the config script
run( 'sh configure --with-pbsdir=%s' % os.environ['LIBTORQUE_DIR'], os.getcwd(), 'Running pbs_python configure script' )
+# version string in 2.9.4 setup.py is wrong
+print "scramble(): Patching setup.py"
+if not os.path.exists( 'setup.py.orig' ):
+ shutil.copyfile( 'setup.py', 'setup.py.orig' )
+ i = open( 'setup.py.orig', 'r' )
+ o = open( 'setup.py', 'w' )
+ for line in i.readlines():
+ if line == " version = '2.9.0',\n":
+ line = " version = '2.9.4',\n"
+ print >>o, line,
+i.close()
+o.close()
+
# reset args for distutils
me = sys.argv[0]
sys.argv = [ me ]
1
0
03 Mar '10
details: http://www.bx.psu.edu/hg/galaxy/rev/db7ee1dc19c4
changeset: 3462:db7ee1dc19c4
user: Nate Coraor <nate(a)bx.psu.edu>
date: Tue Mar 02 11:52:16 2010 -0500
description:
Scratch that, just upgrade pbs_python instead
diffstat:
eggs.ini | 2 +-
lib/galaxy/eggs/scramble.py | 2 +-
scripts/scramble/patches/pbs_python/setup.py | 64 ----------------------------
scripts/scramble/scripts/pbs_python.py | 3 -
4 files changed, 2 insertions(+), 69 deletions(-)
diffs (105 lines):
diff -r cb10a08016eb -r db7ee1dc19c4 eggs.ini
--- a/eggs.ini Tue Mar 02 11:37:55 2010 -0500
+++ b/eggs.ini Tue Mar 02 11:52:16 2010 -0500
@@ -16,7 +16,7 @@
Cheetah = 2.2.2
DRMAA_python = 0.2
MySQL_python = 1.2.3c1
-pbs_python = 2.9.4
+pbs_python = 2.9.8
psycopg2 = 2.0.6
pycrypto = 2.0.1
pysam = 0.1.1
diff -r cb10a08016eb -r db7ee1dc19c4 lib/galaxy/eggs/scramble.py
--- a/lib/galaxy/eggs/scramble.py Tue Mar 02 11:37:55 2010 -0500
+++ b/lib/galaxy/eggs/scramble.py Tue Mar 02 11:52:16 2010 -0500
@@ -56,7 +56,7 @@
self.run_scramble_script()
new_egg = os.path.join( self.buildpath, 'dist', os.path.basename( self.distribution.location ) )
if not os.path.exists( new_egg ):
- raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n %s" % ( sys._getframe().f_code.co_name, self.name, egg_name ) )
+ raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n %s" % ( sys._getframe().f_code.co_name, self.name, new_egg ) )
shutil.copyfile( new_egg, self.distribution.location )
log.warning( "%s(): Copied egg to:" % sys._getframe().f_code.co_name )
log.warning( " %s" % self.distribution.location )
diff -r cb10a08016eb -r db7ee1dc19c4 scripts/scramble/patches/pbs_python/setup.py
--- a/scripts/scramble/patches/pbs_python/setup.py Tue Mar 02 11:37:55 2010 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-#!/usr/bin/env python
-#
-# $Id: setup.py 434 2005-11-04 15:02:07Z bas $
-#
-# set ts=4
-#
-
-import sys
-import os
-
-from distutils.core import setup, Extension
-
-# Try some usefule defaults if not set
-#
-PBS_LIB_DIR='/opt/local/lib'
-NEW_BUILD_SYSTEM=1
-
-if not PBS_LIB_DIR:
- for dir in ['/usr/lib', '/usr/local/lib', '/opt/pbs/usr/lib', '/usr/lib/torque', '/opt/pbs/lib', '/opt/torque/lib' ]:
- dummy_new = os.path.join(dir, 'libtorque.so')
- dummy_old = os.path.join(dir, 'libpbs.a')
- if os.path.exists(dummy_new):
- PBS_LIB_DIR=dir
- break
- elif os.path.exists(dummy_old):
- PBS_LIB_DIR=dir
- NEW_BUILD_SYSTEM=0
- break
-
-if not PBS_LIB_DIR:
- print 'Please specify where the PBS libraries are!!'
- print 'edit setup.py and fill in the PBS_LIB_DIR variable'
- sys.exit(1)
-
-# Test if we have all the libs:
-#
-if NEW_BUILD_SYSTEM:
- LIBS = ['torque']
-else:
- LIBS = ['log', 'net', 'pbs']
- for lib in LIBS:
- library = 'lib%s.a' %(lib)
- dummy = os.path.join(PBS_LIB_DIR, library)
- if not os.path.exists(dummy):
- print 'You need to install "%s" in %s' %(library, PBS_LIB_DIR)
- sys.exit(1)
-
-setup ( name = 'pbs_python',
- version = '2.9.4',
- description = 'openpbs/torque python interface',
- author = 'Bas van der Vlies',
- author_email = 'basv(a)sara.nl',
- url = 'http://www.sara.nl/index_eng.html',
-
- extra_path = 'pbs',
- package_dir = { '' : 'src' },
- py_modules = [ 'pbs', 'PBSQuery' ],
-
- ext_modules = [
- Extension( '_pbs', ['src/pbs_wrap.c'],
- library_dirs = [ PBS_LIB_DIR ],
- libraries = LIBS)
- ]
-)
diff -r cb10a08016eb -r db7ee1dc19c4 scripts/scramble/scripts/pbs_python.py
--- a/scripts/scramble/scripts/pbs_python.py Tue Mar 02 11:37:55 2010 -0500
+++ b/scripts/scramble/scripts/pbs_python.py Tue Mar 02 11:52:16 2010 -0500
@@ -19,9 +19,6 @@
# the build process doesn't set an rpath for libtorque
os.environ['LD_RUN_PATH'] = os.environ['LIBTORQUE_DIR']
-# patch setup.py
-shutil.copy( os.path.join( patches, 'pbs_python', 'setup.py' ), 'setup.py' )
-
# run the config script
run( 'sh configure --with-pbsdir=%s' % os.environ['LIBTORQUE_DIR'], os.getcwd(), 'Running pbs_python configure script' )
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03 Mar '10
details: http://www.bx.psu.edu/hg/galaxy/rev/cb10a08016eb
changeset: 3461:cb10a08016eb
user: Nate Coraor <nate(a)bx.psu.edu>
date: Tue Mar 02 11:37:55 2010 -0500
description:
Use the old method for fixing pbs_python's version
diffstat:
scripts/scramble/patches/pbs_python/setup.py | 64 ++++++++++++++++++++++++++++
scripts/scramble/scripts/pbs_python.py | 7 +-
2 files changed, 68 insertions(+), 3 deletions(-)
diffs (102 lines):
diff -r 182a7947e63a -r cb10a08016eb scripts/scramble/patches/pbs_python/setup.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/scramble/patches/pbs_python/setup.py Tue Mar 02 11:37:55 2010 -0500
@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+#
+# $Id: setup.py 434 2005-11-04 15:02:07Z bas $
+#
+# set ts=4
+#
+
+import sys
+import os
+
+from distutils.core import setup, Extension
+
+# Try some usefule defaults if not set
+#
+PBS_LIB_DIR='/opt/local/lib'
+NEW_BUILD_SYSTEM=1
+
+if not PBS_LIB_DIR:
+ for dir in ['/usr/lib', '/usr/local/lib', '/opt/pbs/usr/lib', '/usr/lib/torque', '/opt/pbs/lib', '/opt/torque/lib' ]:
+ dummy_new = os.path.join(dir, 'libtorque.so')
+ dummy_old = os.path.join(dir, 'libpbs.a')
+ if os.path.exists(dummy_new):
+ PBS_LIB_DIR=dir
+ break
+ elif os.path.exists(dummy_old):
+ PBS_LIB_DIR=dir
+ NEW_BUILD_SYSTEM=0
+ break
+
+if not PBS_LIB_DIR:
+ print 'Please specify where the PBS libraries are!!'
+ print 'edit setup.py and fill in the PBS_LIB_DIR variable'
+ sys.exit(1)
+
+# Test if we have all the libs:
+#
+if NEW_BUILD_SYSTEM:
+ LIBS = ['torque']
+else:
+ LIBS = ['log', 'net', 'pbs']
+ for lib in LIBS:
+ library = 'lib%s.a' %(lib)
+ dummy = os.path.join(PBS_LIB_DIR, library)
+ if not os.path.exists(dummy):
+ print 'You need to install "%s" in %s' %(library, PBS_LIB_DIR)
+ sys.exit(1)
+
+setup ( name = 'pbs_python',
+ version = '2.9.4',
+ description = 'openpbs/torque python interface',
+ author = 'Bas van der Vlies',
+ author_email = 'basv(a)sara.nl',
+ url = 'http://www.sara.nl/index_eng.html',
+
+ extra_path = 'pbs',
+ package_dir = { '' : 'src' },
+ py_modules = [ 'pbs', 'PBSQuery' ],
+
+ ext_modules = [
+ Extension( '_pbs', ['src/pbs_wrap.c'],
+ library_dirs = [ PBS_LIB_DIR ],
+ libraries = LIBS)
+ ]
+)
diff -r 182a7947e63a -r cb10a08016eb scripts/scramble/scripts/pbs_python.py
--- a/scripts/scramble/scripts/pbs_python.py Tue Mar 02 11:17:05 2010 -0500
+++ b/scripts/scramble/scripts/pbs_python.py Tue Mar 02 11:37:55 2010 -0500
@@ -1,4 +1,4 @@
-import os, sys
+import os, sys, shutil
if "LIBTORQUE_DIR" not in os.environ:
print "main(): Please set LIBTORQUE_DIR to the path of the"
@@ -13,13 +13,15 @@
sys.path.append( os.path.join( '..', '..', '..', 'lib' ) )
from scramble_lib import *
-ver = get_ver() # get the version
tag = get_tag() # get the tag
clean() # clean up any existing stuff (could happen if you run scramble.py by hand)
# the build process doesn't set an rpath for libtorque
os.environ['LD_RUN_PATH'] = os.environ['LIBTORQUE_DIR']
+# patch setup.py
+shutil.copy( os.path.join( patches, 'pbs_python', 'setup.py' ), 'setup.py' )
+
# run the config script
run( 'sh configure --with-pbsdir=%s' % os.environ['LIBTORQUE_DIR'], os.getcwd(), 'Running pbs_python configure script' )
@@ -27,7 +29,6 @@
me = sys.argv[0]
sys.argv = [ me ]
sys.argv.append( "egg_info" )
-sys.argv.append( "--version=%s" % ver )
if tag is not None:
sys.argv.append( "--tag-build=%s" %tag )
# svn revision (if any) is handled directly in tag-build
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