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Changed Lastz call for tabular (general) format to suppress header

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This commit is contained in:
Kelly Vincent
2009-12-07 15:57:06 -05:00
parent d921aace49
commit f77f919f12
2 changed files with 14 additions and 4 deletions
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tools/sr_mapping/lastz_wrapper.py
+2 -2
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@@ -2,7 +2,7 @@
"""
Runs Lastz
Written for Lastz v. 1.01.86.
Written for Lastz v. 1.01.88.
usage: lastz_wrapper.py [options]
--ref_name: The reference name to change all output matches to
@@ -132,7 +132,7 @@ def __main__():
input2 = options.input2
if options.format == 'tabular':
# Change output format to general if it's tabular and add field names for tabular output
format = 'general'
format = 'general-'
tabular_fields = ':score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle'
elif options.format == 'sam':
# We currently ALWAYS suppress SAM headers.
tools/sr_mapping/lastz_wrapper.xml
+12 -2
View File
@@ -1,4 +1,4 @@
<tool id="lastz_wrapper_2" name="Lastz" version="1.0.0">
<tool id="lastz_wrapper_2" name="Lastz" version="1.1.0">
<description> map short reads against reference sequence</description>
<command interpreter="python">lastz_wrapper.py
#if $seq_name.how_to_name=="yes":
@@ -179,7 +179,17 @@
<param name="num_threads" value="4" />
<output name="output1" file="lastz_wrapper_out3.tabular" />
</test>
<test>
<test>
<!--
Lastz command: first you will need to split the file phiX_split.fasta into two files,
phiX1.fasta and phiX2.fasta, each with 1 sequence (phiX1 and phiX2, respectively). Then:
lastz phiX1.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle > lastz_wrapper_out4.tabular
lastz phiX2.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle >> lastz_wrapper_out4.tabular
You need to point to phiX1.fasta and phiX2.fasta somewhere on your system.
phiX_split.fasta and b1.fasta are located in galaxy's test-data
You will have to replace all the asterisks before the commands with 2 dashes,
as double-dash can't appear in an XML comment
-->
<param name="input2" value="b1.fasta" ftype="fasta" />
<param name="ref_source" value="history" />
<param name="input1" value="phiX_split.fasta" ftype="fasta" />