def headers_ok(fasta): ok = True replicons = common.read_replicon_names(fasta) for replicon in replicons.values(): if "|" in replicon: ok = False return ok
def main(): # Get command line options opts, args = init_options() infiles = args # Input validation for infile in infiles: if not os.path.isfile(infile): print "Input file " + infile + " not found" exit(1) annofile_list = opts.annofiles.split(",") replicons = common.read_replicon_names(opts.reference_fa) if len(replicons) != len(annofile_list): print "Number of annotation files must match the number of sequences in the reference fasta" exit(1) process(infiles, opts, replicons)
def main(): # Get command line options opts, args = init_options() print "Annotating " + opts.infile all_replicons = common.read_replicon_names(opts.fasta) # Separate multiple annotation files annofile_list = opts.annofiles.split(",") if len(annofile_list) != len(all_replicons): print "ERROR: wrong number of replicon names for replicon files" exit(1) print "Using " + str(len(annofile_list)) + " .ptt files" annotations = common.read_annotations(annofile_list, all_replicons) lines_written = write_annotated(opts.infile, opts.outfile, annotations) print str(lines_written) + " lines written to " + opts.outfile
def main(): # Get command line options opts, args = init_options() print "Tabulating " + opts.infile all_replicons = common.read_replicon_names(opts.fasta) # Separate multiple annotation files annofile_list = opts.annofiles.split(",") if len(annofile_list) != len(all_replicons): print "ERROR: wrong number of replicon names for replicon files" exit(1) print "Using annotation files " + str(annofile_list) annotations = common.read_annotations(annofile_list, all_replicons) (runs, hits, allhits) = read_hits_file(opts.infile) lines_written = write_tabulated(opts.outfile, runs, annotations, hits, allhits)