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
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
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