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Add option for writing not aligned reads to file

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Reviewed-by: Nicola Soranzo <soranzo@crs4.it>
This commit is contained in:
Andrea Sbardellati
2013-01-18 17:11:04 +01:00
parent f3f4ef46ee
commit 47630c9ed6
2 changed files with 61 additions and 4 deletions
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tools/sr_mapping/bowtie2_wrapper.py
+31 -2
View File
@@ -31,10 +31,29 @@ def __main__():
parser.add_option( '', '--rgpl', dest='rgpl', help='Platform/technology used to produce the reads' )
parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' )
parser.add_option( '', '--output_unaligned_reads', dest='output_unaligned_reads', help='File name for unaligned reads (single-end)' )
parser.add_option( '', '--output_unaligned_reads_l', dest='output_unaligned_reads_l', help='File name for unaligned reads (left, paired-end)' )
parser.add_option( '', '--output_unaligned_reads_r', dest='output_unaligned_reads_r', help='File name for unaligned reads (right, paired-end)' )
(options, args) = parser.parse_args()
tmp_unaligned_file_name = None
# Creat bowtie index if necessary.
tmp_index_dir = tempfile.mkdtemp()
if options.single_paired == 'paired':
if options.output_unaligned_reads_l and options.output_unaligned_reads_r:
tmp_unaligned_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
tmp_unaligned_file_name = tmp_unaligned_file.name
tmp_unaligned_file.close()
output_unaligned_reads = '--un-conc %s' % tmp_unaligned_file_name
else:
output_unaligned_reads = ''
elif options.output_unaligned_reads:
output_unaligned_reads = '--un %s' % options.output_unaligned_reads
else:
output_unaligned_reads = ''
if options.own_file:
index_path = os.path.join( tmp_index_dir, '.'.join( os.path.split( options.own_file )[1].split( '.' )[:-1] ) )
try:
@@ -71,7 +90,7 @@ def __main__():
index_path = options.index_path
# Build bowtie command; use view and sort to create sorted bam.
cmd = 'bowtie2 %s -x %s %s | samtools view -Su - | samtools sort -o - - > %s'
cmd = 'bowtie2 %s -x %s %s %s | samtools view -Su - | samtools sort -o - - > %s'
# Set up reads.
if options.single_paired == 'paired':
@@ -104,7 +123,7 @@ def __main__():
opts += ' --rg %s:%s' % ( 'SM', options.rgsm )
# Final command:
cmd = cmd % ( opts, index_path, reads, options.output )
cmd = cmd % ( opts, index_path, reads, output_unaligned_reads, options.output )
print cmd
# Run
@@ -136,6 +155,16 @@ def __main__():
except Exception, e:
stop_err( 'Error in bowtie2:\n' + str( e ) )
# get unaligned reads output files in place if appropriate
if options.single_paired == 'paired' and tmp_unaligned_file_name and options.output_unaligned_reads_l and options.output_unaligned_reads_r:
try:
left = tmp_unaligned_file_name.replace( '.fastq', '.1.fastq' )
right = tmp_unaligned_file_name.replace( '.fastq', '.2.fastq' )
shutil.move( left, options.output_unaligned_reads_l )
shutil.move( right, options.output_unaligned_reads_r )
except Exception, e:
sys.stdout.write( 'Error producing the unaligned output files.\n' )
# Clean up temp dirs
if os.path.exists( tmp_index_dir ):
shutil.rmtree( tmp_index_dir )
tools/sr_mapping/bowtie2_wrapper.xml
+30 -2
View File
@@ -1,6 +1,6 @@
<tool id="bowtie2" name="Bowtie2" version="0.1">
<!-- Wrapper compatible with Bowtie version 2.0.0 -->
<description>is a short-read mapper</description>
<description>is a short-read aligner</description>
<version_command>bowtie2 --version</version_command>
<requirements>
<requirement type="package">bowtie2</requirement>
@@ -15,6 +15,17 @@
## Outputs.
--output=$output
#if str( $singlePaired.sPaired ) == "single"
#if $output_unaligned_reads_l
--output_unaligned_reads=$output_unaligned_reads_l
#end if
#else
#if $output_unaligned_reads_l and $output_unaligned_reads_r
--output_unaligned_reads_l=$output_unaligned_reads_l
--output_unaligned_reads_r=$output_unaligned_reads_r
#end if
#end if
## Handle reference file.
#if $refGenomeSource.genomeSource == "history":
--own-file=$refGenomeSource.ownFile
@@ -71,6 +82,7 @@
<param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" />
</when>
</conditional>
<param name="unalignedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (uses --un for single-end and --un-conc for paired-ends)" />
<conditional name="refGenomeSource">
<param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
<option value="indexed">Use a built-in index</option>
@@ -133,7 +145,7 @@
</inputs>
<outputs>
<data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
<data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
@@ -152,6 +164,22 @@
</conditional>
</actions>
</data>
<data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
<filter>unalignedFile is True</filter>
<actions>
<action type="format">
<option type="from_param" name="singlePaired.input1" param_attribute="ext" />
</action>
</actions>
</data>
<data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
<filter>singlePaired['sPaired'] == "paired" and unalignedFile is True</filter>
<actions>
<action type="format">
<option type="from_param" name="singlePaired.input1" param_attribute="ext" />
</action>
</actions>
</data>
</outputs>
<tests>