Ejemplo n.º 1
0
def prepare_for_Gibscluster(exe, workdir, pepseq, lengths=[8, 9, 10, 11]):
    commands = []
    outfiles = []

    fck = pso.maketxtfile(workdir, 'gibbs_in', 'pep', 'All')
    pso.mywrite(fck, pepseq)

    for length in lengths:
        outfile = pso.maketxtfile(workdir, 'gibbs_out', 'gibbs', length)
        command = "{exe} -fast -l {length} -s -1 {infile} > {outfile}".format(
            exe=exe, length=length, infile=fck, outfile=outfile)

        outfiles.append(outfile)
        commands.append(command)
    return outfiles, commands
Ejemplo n.º 2
0
def prepare_for_Gibscluster(exe, workdir, pepseq, lengths=[8, 9, 10, 11]):
    commands = []
    outfiles = []

    fck = pso.maketxtfile(workdir, 'gibbs_in', 'pep', 'All')
    pso.mywrite(fck, pepseq)

    for length in lengths:
        outfile = pso.maketxtfile(workdir, 'gibbs_out', 'gibbs', length)
        command = "{exe} -fast -l {length} -s -1 {infile} > {outfile}".format(exe=exe,
                                                                              length=length,
                                                                              infile=fck,
                                                                              outfile=outfile)

        outfiles.append(outfile)
        commands.append(command)
    return outfiles, commands
Ejemplo n.º 3
0
def prepare_for_Gibscluster2(exe, workdir, pepseq, length=8):
    commands = []
    outfiles = []

    for key, pepseq in pepseq.items():
        print key
        key = key.replace(":", "-")
        fck = pso.maketxtfile(workdir, 'gibbs_in_', 'pep', key)
        pso.mywrite(fck, pepseq)

        outfile = pso.maketxtfile(workdir, 'gibbs_out_', 'gibbs', key)
        command = "{exe} -fast -l {length} -s -1 {infile} > {outfile}".format(exe=exe,
                                                                              length=length,
                                                                              infile=fck,
                                                                              outfile=outfile)

        outfiles.append(outfile)
        commands.append(command)
    return outfiles, commands
Ejemplo n.º 4
0
def prepare_for_Gibscluster2(exe, workdir, pepseq, length=8):
    commands = []
    outfiles = []

    for key, pepseq in pepseq.items():
        print key
        key = key.replace(":", "-")
        fck = pso.maketxtfile(workdir, 'gibbs_in_', 'pep', key)
        pso.mywrite(fck, pepseq)

        outfile = pso.maketxtfile(workdir, 'gibbs_out_', 'gibbs', key)
        command = "{exe} -fast -l {length} -s -1 {infile} > {outfile}".format(exe=exe,
                                                                              length=length,
                                                                              infile=fck,
                                                                              outfile=outfile)

        outfiles.append(outfile)
        commands.append(command)
    return outfiles, commands