[galaxy-dev] [hg] galaxy 3440: Update Combine FASTA and QUAL tool to allow th...

25 Feb 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/674aaee19991
changeset: 3440:674aaee19991
user:      Dan Blankenberg <dan@bx.psu.edu>
date:      Wed Feb 24 16:50:06 2010 -0500
description:
Update Combine FASTA and QUAL tool to allow the quality score file to be optional.

When not provided, the output will be fastqsanger or fastqsolid (when a csfasta is provided) with each quality score being the maximal allowed value (93).

diffstat:

 lib/galaxy_utils/sequence/fasta.py                         |    2 +
 lib/galaxy_utils/sequence/fastq.py                         |   25 +
 test-data/fastq_combiner_no_qual_ascii_out_1.fastqsolid    |  576 +++++++++++++
 test-data/fastq_combiner_no_qual_decimal_out_1.fastqsanger |   12 +
 tools/fastq/fastq_combiner.py                              |   11 +-
 tools/fastq/fastq_combiner.xml                             |   16 +-
 6 files changed, 637 insertions(+), 5 deletions(-)

diffs (725 lines):

diff -r 46849d69d7e6 -r 674aaee19991 lib/galaxy_utils/sequence/fasta.py

--- a/lib/galaxy_utils/sequence/fasta.py	Wed Feb 24 16:48:22 2010 -0500
+++ b/lib/galaxy_utils/sequence/fasta.py	Wed Feb 24 16:50:06 2010 -0500
@@ -53,6 +53,8 @@
     def close( self ):
         return self.file.close()
     def get( self, sequence_id ):
+        if not isinstance( sequence_id, basestring ):
+            sequence_id = sequence_id.identifier
         rval = None
         if sequence_id in self.offset_dict:
             initial_offset = self.file.tell()
diff -r 46849d69d7e6 -r 674aaee19991 lib/galaxy_utils/sequence/fastq.py
--- a/lib/galaxy_utils/sequence/fastq.py	Wed Feb 24 16:48:22 2010 -0500
+++ b/lib/galaxy_utils/sequence/fastq.py	Wed Feb 24 16:50:06 2010 -0500
@@ -3,6 +3,7 @@
 import string
 import transform
 from sequence import SequencingRead
+from fasta import fastaSequence
 
 class fastqSequencingRead( SequencingRead ):
     format = 'sanger' #sanger is default
@@ -456,6 +457,8 @@
     def close( self ):
         return self.file.close()
     def get( self, sequence_id ):
+        if not isinstance( sequence_id, basestring ):
+            sequence_id = sequence_id.identifier
         rval = None
         if sequence_id in self.offset_dict:
             initial_offset = self.file.tell()
@@ -593,3 +596,25 @@
         fastq_read.sequence = fasta_seq.sequence
         fastq_read.quality = quality_seq.sequence
         return fastq_read
+
+class fastqFakeFastaScoreReader( object ):
+    def __init__( self, format = 'sanger', quality_encoding = None ):
+        self.fastq_read = fastqSequencingRead.get_class_by_format( format )()
+        if quality_encoding != 'decimal':
+            quality_encoding = 'ascii'
+        self.quality_encoding = quality_encoding
+    def close( self ):
+        return #nothing to close
+    def get( self, sequence ):
+        assert isinstance( sequence, fastaSequence ), 'fastqFakeFastaScoreReader requires a fastaSequence object as the parameter'
+        #add sequence to fastq_read, then get_sequence(), color space adapters do not have quality score values
+        self.fastq_read.sequence = sequence.sequence
+        new_sequence = fastaSequence()
+        new_sequence.identifier = sequence.identifier
+        if self.quality_encoding == 'ascii':
+            new_sequence.sequence = chr( self.fastq_read.ascii_max ) * len( self.fastq_read.get_sequence() )
+        else:
+            new_sequence.sequence = ( "%i " % self.fastq_read.quality_max ) * len( self.fastq_read.get_sequence() )
+        return new_sequence
+    def has_data( self ):
+        return '' #No actual data exist, none can be remaining
diff -r 46849d69d7e6 -r 674aaee19991 test-data/fastq_combiner_no_qual_ascii_out_1.fastqsolid
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_combiner_no_qual_ascii_out_1.fastqsolid	Wed Feb 24 16:50:06 2010 -0500
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diff -r 46849d69d7e6 -r 674aaee19991 test-data/fastq_combiner_no_qual_decimal_out_1.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_combiner_no_qual_decimal_out_1.fastqsanger	Wed Feb 24 16:50:06 2010 -0500
@@ -0,0 +1,12 @@
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++
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++
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diff -r 46849d69d7e6 -r 674aaee19991 tools/fastq/fastq_combiner.py
--- a/tools/fastq/fastq_combiner.py	Wed Feb 24 16:48:22 2010 -0500
+++ b/tools/fastq/fastq_combiner.py	Wed Feb 24 16:50:06 2010 -0500
@@ -1,6 +1,6 @@
 #Dan Blankenberg
 import sys, os, shutil
-from galaxy_utils.sequence.fastq import fastqWriter, fastqSequencingRead, fastqCombiner
+from galaxy_utils.sequence.fastq import fastqWriter, fastqSequencingRead, fastqCombiner, fastqFakeFastaScoreReader
 from galaxy_utils.sequence.fasta import fastaReader, fastaNamedReader
 
 def main():
@@ -23,15 +23,18 @@
         format = 'illumina'
     
     out = fastqWriter( open( output_filename, 'wb' ), format = format, force_quality_encoding = force_quality_encoding )
-    qual_input = fastaNamedReader( open( qual_filename, 'rb' )  )
+    if qual_filename == 'None':
+        qual_input = fastqFakeFastaScoreReader( format, quality_encoding = force_quality_encoding )
+    else:
+        qual_input = fastaNamedReader( open( qual_filename, 'rb' )  )
+    
     fastq_combiner = fastqCombiner( format )
     i = None
     skip_count = 0
     for i, sequence in enumerate( fastaReader( open( fasta_filename, 'rb' ) ) ):
-        quality = qual_input.get( sequence.identifier )
+        quality = qual_input.get( sequence )
         if quality:
             fastq_read = fastq_combiner.combine( sequence, quality )
-            #Should we check that fastq read is valid? for now, assume groomer will be used to verify
             out.write( fastq_read )
         else:
             skip_count += 1
diff -r 46849d69d7e6 -r 674aaee19991 tools/fastq/fastq_combiner.xml
--- a/tools/fastq/fastq_combiner.xml	Wed Feb 24 16:48:22 2010 -0500
+++ b/tools/fastq/fastq_combiner.xml	Wed Feb 24 16:50:06 2010 -0500
@@ -3,7 +3,7 @@
   <command interpreter="python">fastq_combiner.py '$fasta_file' '${fasta_file.extension}' '$qual_file' '${qual_file.extension}' '$output_file' '$force_quality_encoding'</command>
   <inputs>
     <param name="fasta_file" type="data" format="fasta,csfasta" label="FASTA File" />
-    <param name="qual_file" type="data" format="qual" label="Quality Score File" />
+    <param name="qual_file" type="data" format="qual" label="Quality Score File" optional="True" />
     <param name="force_quality_encoding" type="select" label="Force Quality Score encoding">
       <option value="None">Use Source Encoding</option>
       <option value="ascii" selected="True">ASCII</option>
@@ -45,11 +45,25 @@
       <param name="force_quality_encoding" value="decimal" />
       <output name="output_file" file="wrapping_as_sanger_decimal.fastqsanger" />
     </test>
+    <test>
+      <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
+      <param name="qual_file" />
+      <param name="force_quality_encoding" value="decimal" />
+      <output name="output_file" file="fastq_combiner_no_qual_decimal_out_1.fastqsanger" />
+    </test>
+    <test>
+      <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
+      <param name="qual_file" />
+      <param name="force_quality_encoding" value="ascii" />
+      <output name="output_file" file="fastq_combiner_no_qual_ascii_out_1.fastqsolid" />
+    </test>
   </tests>
   <help>
 **What it does**
 
 This tool joins a FASTA file to a Quality Score file, creating a single FASTQ block for each read.
 
+Specifying a set of quality scores is optional; when not provided, the output will be fastqsanger or fastqsolid (when a csfasta is provided) with each quality score being the maximal allowed value (93).
+
   </help>
 </tool>

    

[galaxy-dev] [hg] galaxy 3440: Update Combine FASTA and QUAL tool to allow th...

Greg Von Kuster