details:
http://www.bx.psu.edu/hg/galaxy/rev/cbdd394a265c
changeset: 2503:cbdd394a265c
user: Kelly Vincent <kpvincent(a)bx.psu.edu>
date: Fri Jul 24 17:06:12 2009 -0400
description:
Removed option to select indexing algorithm from BWA wrapper and have it automatically
determine the algorithm by file size.
2 file(s) affected in this change:
tools/sr_mapping/bwa_wrapper.py
tools/sr_mapping/bwa_wrapper.xml
diffs (76 lines):
diff -r 472bc69143be -r cbdd394a265c tools/sr_mapping/bwa_wrapper.py
--- a/tools/sr_mapping/bwa_wrapper.py Fri Jul 24 16:39:48 2009 -0400
+++ b/tools/sr_mapping/bwa_wrapper.py Fri Jul 24 17:06:12 2009 -0400
@@ -17,7 +17,6 @@
#Parse Command Line
parser = optparse.OptionParser()
parser.add_option('', '--ref', dest='ref', help='The
reference genome to use or index')
- parser.add_option('', '--indexingAlg', dest='indexingAlg',
help='The algorithm to use while indexing')
parser.add_option('', '--fastq', dest='fastq', help='The
(forward) fastq file to use for the mapping')
parser.add_option('', '--rfastq', dest='rfastq',
help='The reverse fastq file to use for mapping if paired-end data')
parser.add_option('', '--output', dest='output',
help='The file to save the output (SAM format)')
@@ -53,10 +52,18 @@
os.system('cp %s %s' % (options.ref, tmp_dir))
except Exception, erf:
stop_err('Error creating temp directory for indexing purposes\n' +
str(erf))
+ try:
+ size = os.stat(options.ref).st_size
+ if size <= 2**30:
+ indexingAlg = 'is'
+ else:
+ indexingAlg = 'bwtsw'
+ except:
+ indexingAlg = 'is'
if options.fileType == 'solid':
- indexing_cmds = '-c -a %s' % options.indexingAlg
+ indexing_cmds = '-c -a %s' % indexingAlg
else:
- indexing_cmds = '-a %s' % options.indexingAlg
+ indexing_cmds = '-a %s' % indexingAlg
options.ref = os.path.join(tmp_dir,os.path.split(options.ref)[1])
cmd1 = 'bwa index %s %s 2> /dev/null' % (indexing_cmds, options.ref)
try:
diff -r 472bc69143be -r cbdd394a265c tools/sr_mapping/bwa_wrapper.xml
--- a/tools/sr_mapping/bwa_wrapper.xml Fri Jul 24 16:39:48 2009 -0400
+++ b/tools/sr_mapping/bwa_wrapper.xml Fri Jul 24 17:06:12 2009 -0400
@@ -4,10 +4,8 @@
bwa_wrapper.py
#if $solidOrSolexa.solidRefGenomeSource.refGenomeSource == "history":
--ref=$solidOrSolexa.solidRefGenomeSource.ownFile
- --indexingAlg=$solidOrSolexa.solidRefGenomeSource.algorithm
#else:
--ref=$solidOrSolexa.solidRefGenomeSource.indices.value
- --indexingAlg="None"
#end if
--fastq=$paired.input1
#if $paired.sPaired == "paired":
@@ -74,10 +72,6 @@
</param>
<when value="history">
<param name="ownFile" type="data" label="Select a
reference genome" />
- <param name="algorithm" type="select" label="Select
an indexing algorithm" help="IS works on databses 2GB or less, and is
linear-time. BWT-SW works on database 10MB and larger, and trades speed for
memory.">
- <option value="is">IS</option>
- <option value="bwtsw">BWT-SW</option>
- </param>
</when>
<when value="indexed">
<param name="indices" type="select" label="Select a
reference genome">
@@ -98,10 +92,6 @@
</param>
<when value="history">
<param name="ownFile" type="data" label="Select a
reference genome" />
- <param name="algorithm" type="select" label="Select
an indexing algorithm" help="IS works on databses 2GB or less, and is
linear-time. BWT-SW works on database 10MB and larger, and trades speed for
memory.">
- <option value="is">IS</option>
- <option value="bwtsw">BWT-SW</option>
- </param>
</when>
<when value="indexed">
<param name="indices" type="select" label="Select a
reference genome">
@@ -177,7 +167,6 @@
<param name="solidSolexa" value="solid" />
<param name="refGenomeSource" value="history" />
<param name="ownFile" value="phiX.fa" />
- <param name="algorithm" value="is" />
<param name="sPaired" value="single" />
<param name="input1" value="bwa_phiX_sanger.fastq" />
<param name="source_select" value="pre_set" />