details: http://www.bx.psu.edu/hg/galaxy/rev/119315b57656 changeset: 3154:119315b57656 user: Kelly Vincent kpvincent@bx.psu.edu date: Mon Dec 07 15:57:06 2009 -0500 description: Changed Lastz call for tabular (general) format to suppress header
diffstat:
test-data/lastz_wrapper_out4.tabular | 2 -- tools/sr_mapping/lastz_wrapper.py | 4 ++-- tools/sr_mapping/lastz_wrapper.xml | 14 ++++++++++++-- 3 files changed, 14 insertions(+), 6 deletions(-)
diffs (65 lines):
diff -r 14214b45db3f -r 119315b57656 test-data/lastz_wrapper_out4.tabular --- a/test-data/lastz_wrapper_out4.tabular Mon Dec 07 14:45:47 2009 -0500 +++ b/test-data/lastz_wrapper_out4.tabular Mon Dec 07 15:57:06 2009 -0500 @@ -1,4 +1,3 @@ -#score name1 strand1 size1 start1 zstart1 end1 length1 text1 name2 strand2 size2 start2 zstart2 end2 start2+ zstart2+ end2+ length2 text2 diff cigar identity idPct coverage covPct gaprate gapPct diagonal shingle 36 phiX1 + 2310 229 228 264 36 GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 228 NA 36 phiX1 + 2310 2071 2070 2106 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2070 NA 35 phiX1 + 2310 1067 1066 1101 35 GGTCAGATTGGTCGTCTTATTACCATTTCAACTAC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GGTCAGATTGGTCGTCTTATTACCATTTCAACTAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1065 NA @@ -207,7 +206,6 @@ 36 phiX1 + 2310 333 332 368 36 AGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 332 NA 36 phiX1 + 2310 72 71 107 36 ATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 71 NA 36 phiX1 + 2310 1974 1973 2009 36 CGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1973 NA -#score name1 strand1 size1 start1 zstart1 end1 length1 text1 name2 strand2 size2 start2 zstart2 end2 start2+ zstart2+ end2+ length2 text2 diff cigar identity idPct coverage covPct gaprate gapPct diagonal shingle 35 phiX2 + 3076 1985 1984 2019 35 CCCCCAACTTGATATTAATAACACTATAGACCACC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CCCCCAACTTGATATTAATAACACTATAGACCACC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1983 NA 36 phiX2 + 3076 1212 1211 1247 36 ATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1211 NA 33 phiX2 + 3076 2253 2252 2285 33 GGTTGGTTTATCGTTTTTGACACTCTCACGTTG HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GGTTGGTTTATCGTTTTTGACACTCTCACGTTG ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 2252 NA diff -r 14214b45db3f -r 119315b57656 tools/sr_mapping/lastz_wrapper.py --- a/tools/sr_mapping/lastz_wrapper.py Mon Dec 07 14:45:47 2009 -0500 +++ b/tools/sr_mapping/lastz_wrapper.py Mon Dec 07 15:57:06 2009 -0500 @@ -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 @@ 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. diff -r 14214b45db3f -r 119315b57656 tools/sr_mapping/lastz_wrapper.xml --- a/tools/sr_mapping/lastz_wrapper.xml Mon Dec 07 14:45:47 2009 -0500 +++ b/tools/sr_mapping/lastz_wrapper.xml Mon Dec 07 15:57:06 2009 -0500 @@ -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" />