Mercurial > repos > drosofff > bowtie_for_smallrna
changeset 4:303baef87cb7 draft
Uploaded
| author | drosofff |
|---|---|
| date | Sat, 21 Jun 2014 09:54:35 -0400 |
| parents | 97da5d474800 |
| children | 0577105049bd |
| files | sRbowtie/sRbowtie.py |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/sRbowtie/sRbowtie.py Sat Jun 21 09:54:07 2014 -0400 +++ b/sRbowtie/sRbowtie.py Sat Jun 21 09:54:35 2014 -0400 @@ -1,9 +1,9 @@ #!/usr/bin/env python # small RNA oriented bowtie wrapper -# version 1 19-5-2014 +# version 1.01 29-5-2014 # Usage sRbowtie.py <1 input_fasta_file> <2 alignment method> <3 -v mismatches> <4 out_type> <5 buildIndexIfHistory> <6 fasta/bowtie index> <7 bowtie output> <8 ali_fasta> <9 unali_fasta> <10 --num-threads \${GALAXY_SLOTS:-4}> +# current rev: for bowtie __norc, move from --supress 2,6,7,8 to --supress 6,7,8. Future Parser must be updated to take into account this standardisation # To Do: -# implement number of bowtie processes as a Galaxy env variable # implement an arg parser # Christophe Antoniewski <drosofff@gmail.com> @@ -15,7 +15,7 @@ def bowtieCommandLiner (alignment_method, v_mis, out_type, aligned, unaligned, input, index, output, pslots="12"): if alignment_method=="RNA": - x = "-v %s -M 1 --best --strata -p %s --norc --suppress 2,6,7,8" % (v_mis, pslots) + x = "-v %s -M 1 --best --strata -p %s --norc --suppress 6,7,8" % (v_mis, pslots) elif alignment_method=="unique": x = "-v %s -m 1 -p %s --suppress 6,7,8" % (v_mis, pslots) elif alignment_method=="multiple":