def cufflinks(args):
    """
    %prog cufflinks folder reference

    Run cufflinks on a folder containing tophat results.
    """
    p = OptionParser(cufflinks.__doc__)
    p.add_option("--gtf", help="Reference annotation [default: %default]")
    p.set_cpus()
    opts, args = p.parse_args(args)

    if len(args) != 2:
        sys.exit(not p.print_help())

    folder, reference = args
    cpus = opts.cpus
    gtf = opts.gtf
    transcripts = "transcripts.gtf"

    mm = MakeManager()
    gtfs = []
    for bam in iglob(folder, "*.bam"):
        pf = op.basename(bam).split(".")[0]
        outdir = pf + "_cufflinks"
        cmd = "cufflinks"
        cmd += " -o {0}".format(outdir)
        cmd += " -p {0}".format(cpus)
        if gtf:
            cmd += " -g {0}".format(gtf)
        cmd += " --frag-bias-correct {0}".format(reference)
        cmd += " --multi-read-correct"
        cmd += " {0}".format(bam)
        cgtf = op.join(outdir, transcripts)
        mm.add(bam, cgtf, cmd)
        gtfs.append(cgtf)

    assemblylist = "assembly_list.txt"
    cmd = 'find . -name "{0}" > {1}'.format(transcripts, assemblylist)
    mm.add(gtfs, assemblylist, cmd)

    mergedgtf = "merged/merged.gtf"
    cmd = "cuffmerge"
    cmd += " -o merged"
    cmd += " -p {0}".format(cpus)
    if gtf:
        cmd += " -g {0}".format(gtf)
    cmd += " -s {0}".format(reference)
    cmd += " {0}".format(assemblylist)
    mm.add(assemblylist, mergedgtf, cmd)

    mm.write()
def cufflinks ( args ) : p = OptionParser ( cufflinks . __doc__ ) p . add_option ( "--gtf" , help = "Reference annotation [default: %default]" ) p . set_cpus ( ) opts , args = p . parse_args ( args ) if len ( args ) != 2 : sys . exit ( not p . print_help ( ) ) folder , reference = args cpus = opts . cpus gtf = opts . gtf transcripts = "transcripts.gtf" mm = MakeManager ( ) gtfs = [ ] for bam in iglob ( folder , "*.bam" ) : pf = op . basename ( bam ) . split ( "." ) [ 0 ] outdir = pf + "_cufflinks" cmd = "cufflinks" cmd += " -o {0}" . format ( outdir ) cmd += " -p {0}" . format ( cpus ) if gtf : cmd += " -g {0}" . format ( gtf ) cmd += " --frag-bias-correct {0}" . format ( reference ) cmd += " --multi-read-correct" cmd += " {0}" . format ( bam ) cgtf = op . join ( outdir , transcripts ) mm . add ( bam , cgtf , cmd ) gtfs . append ( cgtf ) assemblylist = "assembly_list.txt" cmd = 'find . -name "{0}" > {1}' . format ( transcripts , assemblylist ) mm . add ( gtfs , assemblylist , cmd ) mergedgtf = "merged/merged.gtf" cmd = "cuffmerge" cmd += " -o merged" cmd += " -p {0}" . format ( cpus ) if gtf : cmd += " -g {0}" . format ( gtf ) cmd += " -s {0}" . format ( reference ) cmd += " {0}" . format ( assemblylist ) mm . add ( assemblylist , mergedgtf , cmd ) mm . write ( )
%prog cufflinks folder reference

    Run cufflinks on a folder containing tophat results.