details: http://www.bx.psu.edu/hg/galaxy/rev/ebc1c19fc2d5
changeset: 2875:ebc1c19fc2d5
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Mon Oct 12 16:14:54 2009 -0400
description:
Changed Bowtie so that if alignment parameters cannot be read, it errors out
1 file(s) affected in this change:
tools/sr_mapping/bowtie_wrapper.py
diffs (14 lines):
diff -r 7fd7bbe91838 -r ebc1c19fc2d5 tools/sr_mapping/bowtie_wrapper.py
--- a/tools/sr_mapping/bowtie_wrapper.py Mon Oct 12 14:40:01 2009 -0400
+++ b/tools/sr_mapping/bowtie_wrapper.py Mon Oct 12 16:14:54 2009 -0400
@@ -132,8 +132,8 @@
('','-o %s'%options.offrate)[int(options.offrate)>=0],
('','--seed %s'%options.seed)[int(options.seed)>=0],
options.threads)
- except ValueError:
- aligning_cmds = '-p %s -S' % options.threads
+ except ValueError, erf:
+ stop_err('Something is wrong with the alignment parameters and the alignment could not be run\n' + str(erf))
# prepare actual aligning commands
if options.paired == 'paired':
details: http://www.bx.psu.edu/hg/galaxy/rev/4a3e48e1e8e1
changeset: 2873:4a3e48e1e8e1
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Mon Oct 12 14:04:28 2009 -0400
description:
Changed FASTQ Groomer's handling of Sanger data to output all lines even if only first n are validated
3 file(s) affected in this change:
test-data/fastq_gen_conv_in2.fastq
test-data/fastq_gen_conv_out2.fastqsanger
tools/next_gen_conversion/fastq_gen_conv.py
diffs (74 lines):
diff -r 9d67ae5ecda7 -r 4a3e48e1e8e1 test-data/fastq_gen_conv_in2.fastq
--- a/test-data/fastq_gen_conv_in2.fastq Mon Oct 12 13:19:31 2009 -0400
+++ b/test-data/fastq_gen_conv_in2.fastq Mon Oct 12 14:04:28 2009 -0400
@@ -5,7 +5,7 @@
@seq2
GGGTCTCCCAGAATGATTAGAGCCGTATAGGA
+
-?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]
+?@ABCDEFGHIJK MNOPQRSTUVWXYZ[\\]
@seq3
GCGGTTCAATACGATTACCACCATGATAAATA
+
diff -r 9d67ae5ecda7 -r 4a3e48e1e8e1 test-data/fastq_gen_conv_out2.fastqsanger
--- a/test-data/fastq_gen_conv_out2.fastqsanger Mon Oct 12 13:19:31 2009 -0400
+++ b/test-data/fastq_gen_conv_out2.fastqsanger Mon Oct 12 14:04:28 2009 -0400
@@ -2,11 +2,19 @@
AAAGGTTTCTCTTTTGGAAATATCTAAATCCC
+
!"#$%&\'()*+,-./0123456789:;<=>.
-@seq2
-GGGTCTCCCAGAATGATTAGAGCCGTATAGGA
-+
-?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]
@seq3
GCGGTTCAATACGATTACCACCATGATAAATA
+
?Aa.1ghB2K!#lk(02GY[[II])Kwl+,5M
+@seq4
+AGTCTTTTCCTCTAAAATAACATAGGATACTA
++
+ghY)N375Nh.,Ol>==/<:2#i&d%#KdNII
+@seq5
+GAGGACTCATGGTAGGTATTTTACATGACATT
++
+IIgy%hf6#394bd&hNMWL$OPB63II*,+-
+@seq6
+GGCCTACATTCATTTACGAGACTAATTAGGGA
++
+IIIIIgd6#5%jKO&.,D+s3aW=cdGB#a1$
\ No newline at end of file
diff -r 9d67ae5ecda7 -r 4a3e48e1e8e1 tools/next_gen_conversion/fastq_gen_conv.py
--- a/tools/next_gen_conversion/fastq_gen_conv.py Mon Oct 12 13:19:31 2009 -0400
+++ b/tools/next_gen_conversion/fastq_gen_conv.py Mon Oct 12 14:04:28 2009 -0400
@@ -47,14 +47,15 @@
lines = []
line = fin.readline()
while line:
- if max_blocks >= 0 and block_num > 0 and orig_type == 'sanger' and max_blocks < block_num:
- print 'break'
- break
- if line.strip():
- # the line that starts of a block, with a name
+ if line.strip() and max_blocks >= 0 and block_num > 0 and orig_type == 'sanger' and block_num >= max_blocks:
+ fout.write(line)
+ if line_count % 4 == 0:
+ block_num += 1
+ line_count += 1
+ elif line.strip():
+ # the line that starts a block, with a name
if line_count % 4 == 0 and line.startswith('@'):
lines.append(line)
- block_num += 1
else:
# if we expect a sequence of bases
if line_count % 4 == 1 and all_bases_valid(line.strip()):
@@ -154,6 +155,8 @@
bad_blocks += 1
base_len = -1
lines = []
+ # mark the successful end of a block
+ block_num += 1
line_count += 1
line = fin.readline()
fout.close()
details: http://www.bx.psu.edu/hg/galaxy/rev/109e94372abb
changeset: 2868:109e94372abb
user: Ross Lazarus <ross.lazarus(a)gmail.com>
date: Sun Oct 11 09:45:38 2009 -0400
description:
added 2 valid chars ;| and patch for empty url_paste in composite upload
2 file(s) affected in this change:
lib/galaxy/tools/parameters/grouping.py
lib/galaxy/util/__init__.py
diffs (24 lines):
diff -r 5391edcf618d -r 109e94372abb lib/galaxy/tools/parameters/grouping.py
--- a/lib/galaxy/tools/parameters/grouping.py Sun Oct 11 09:37:43 2009 -0400
+++ b/lib/galaxy/tools/parameters/grouping.py Sun Oct 11 09:45:38 2009 -0400
@@ -226,7 +226,7 @@
if context.get( 'space_to_tab', None ) not in ["None", None]:
space_to_tab = True
file_bunch = get_data_file_filename( data_file, override_name = name, override_info = info )
- if file_bunch.path:
+ if file_bunch.path and url_paste:
if url_paste.strip():
warnings.append( "All file contents specified in the paste box were ignored." )
else: #we need to use url_paste
diff -r 5391edcf618d -r 109e94372abb lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py Sun Oct 11 09:37:43 2009 -0400
+++ b/lib/galaxy/util/__init__.py Sun Oct 11 09:45:38 2009 -0400
@@ -109,7 +109,7 @@
return text
# characters that are valid
-valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!")
+valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!;|")
# characters that are allowed but need to be escaped
mapped_chars = { '>' :'__gt__',