def main (): '''Main''' options = get_opt() try: fh = open(options.infile) except: chilli.print2stderr('Error: can not open file: %s' % (options.infile)) records = FFP.parse(fh) result_fasta_array = convert(records) out = format2fasta(result_fasta_array) if options.outfile == sys.stdout: print out else: fo = open(options.outfile, 'w') fo.write(out) fo.close()
def iupac2normal(seq, prefixes=['']): '''Returns a list containing degenerate nucleic acid sequences based on the IUPAC table Reference: http://lists.open-bio.org/pipermail/biopython/2006-September/003190.html ''' if len(seq) == 0: return prefixes else: first = seq[0] last_seq = seq[1:] new_prefixes = [] for prefix in prefixes: if first in iupac_dict: for base in iupac_dict[first]: new_prefixes.append(prefix + base) else: chilli.print2stderr('Error: not recognized base: %s.' % (first)) return iupac2normal(last_seq, prefixes = new_prefixes)