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)
