| Previous changeset 27:69baebd10e54 (2016-12-07) Next changeset 29:80c4eebf7bc9 (2016-12-08) |
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Commit message:
Uploaded |
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modified:
gene_identification.py shm_csr.xml wrapper.sh |
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| diff -r 69baebd10e54 -r c0ecc31829bd gene_identification.py --- a/gene_identification.py Wed Dec 07 05:30:33 2016 -0500 +++ b/gene_identification.py Wed Dec 07 08:17:09 2016 -0500 |
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| @@ -106,9 +106,6 @@ for i in range(0, len(searchstrings["ce"]) - chunklength + 1, chunklength / 2): compiledregex["ce"].append((re.compile(searchstrings["ce"][i:i+chunklength]), False)) - -print "ce chunks", len(compiledregex["ce"]) - def removeAndReturnMaxIndex(x): #simplifies a list comprehension m = max(x) |
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| diff -r 69baebd10e54 -r c0ecc31829bd shm_csr.xml --- a/shm_csr.xml Wed Dec 07 05:30:33 2016 -0500 +++ b/shm_csr.xml Wed Dec 07 08:17:09 2016 -0500 |
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| @@ -1,7 +1,7 @@ <tool id="shm_csr" name="SHM & CSR pipeline" version="1.0"> <description></description> <command interpreter="bash"> - wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_uniques $class_filter_cond.class_filter $empty_region_filter $fast + wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_uniques $class_filter_cond.class_filter $empty_region_filter $fast </command> <inputs> <param name="in_file" type="data" label="IMGT zip file to be analysed" /> |
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| diff -r 69baebd10e54 -r c0ecc31829bd wrapper.sh --- a/wrapper.sh Wed Dec 07 05:30:33 2016 -0500 +++ b/wrapper.sh Wed Dec 07 08:17:09 2016 -0500 |
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| @@ -10,15 +10,16 @@ include_fr1=$6 functionality=$7 unique=$8 -naive_output_ca=$9 -naive_output_cg=${10} -naive_output_cm=${11} -naive_output_ce=${12} -naive_output_all=${13} -filter_unique=${14} -class_filter=${15} -empty_region_filter=${16} -fast=${17} +naive_output=$9 +naive_output_ca=${10} +naive_output_cg=${11} +naive_output_cm=${12} +naive_output_ce=${13} +naive_output_all=${14} +filter_unique=${15} +class_filter=${16} +empty_region_filter=${17} +fast=${18} mkdir $outdir tar -xzf $dir/style.tar.gz -C $outdir @@ -701,10 +702,13 @@ if [[ "$naive_output" == "yes" ]] then + echo "output naive output" if [[ "${class_filter}" == "101_101" ]] then + echo "copy new_IMGT.txz to ${naive_output_all}" cp $outdir/new_IMGT.txz ${naive_output_all} else + echo "copy for classes" cp $outdir/new_IMGT_IGA.txz ${naive_output_ca} cp $outdir/new_IMGT_IGG.txz ${naive_output_cg} cp $outdir/new_IMGT_IGM.txz ${naive_output_cm} |