comparison sRbowtie/sRbowtie.py @ 4:303baef87cb7 draft

Uploaded

3:97da5d474800

#!/usr/bin/env python
# small RNA oriented bowtie wrapper
# version 1 19-5-2014
# 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}>
# To Do:
# implement number of bowtie processes as a Galaxy env variable
# implement an arg parser
# Christophe Antoniewski <[e-mail]>

import sys, os, subprocess, tempfile, shutil

    sys.stderr.write( '%s\n' % msg )
    sys.exit()

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)
    elif alignment_method=="unique":
        x =  "-v %s -m 1 -p %s --suppress 6,7,8" % (v_mis, pslots)
    elif  alignment_method=="multiple":
        x = "-v %s -M 1 --best --strata -p %s --suppress 6,7,8" % (v_mis, pslots)
    elif alignment_method=="k_option":

4:303baef87cb7

#!/usr/bin/env python
# small RNA oriented bowtie wrapper
# 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 an arg parser
# Christophe Antoniewski <[e-mail]>

import sys, os, subprocess, tempfile, shutil

    sys.stderr.write( '%s\n' % msg )
    sys.exit()

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 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":
        x = "-v %s -M 1 --best --strata -p %s --suppress 6,7,8" % (v_mis, pslots)
    elif alignment_method=="k_option":