def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-pm",
"--profilematrix",
dest="matrixfile",
type="string",
help="name of profile file you want to convert")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
#outf = IOTools.openFile("my_output", "w")
for line in options.matrixfile:
line = line.strip()
fields = line.split()
total = sum([float(col) for col in fields[1:]])
if total == 0:
continue
else:
for i, col in enumerate(fields):
if i == 0: continue
fields[i] = col / total
options.stdout.write("\t".join(map(str, fields)))
for fasta_read in FastaIterator.iterate(IOTools.openFile(
options.fastafile)):
read_sequence = fasta_read.sequence
read_name = fasta_read.title
quals = '.' * len(read_sequence)
new_fastq = Fastq.Record(identifier=read_name,
seq=read_sequence,
quals=quals)
new_fastq.fromPhred([30] * len(read_sequence), format='illumina-1.8')
options.stdout.write(str(new_fastq) + "\n")
# write footer and output benchmark information.
E.Stop()
