qual += chr(int(-10*log10(e)+33))
seq += r2['seq'][N-delta:]
qual += r2['qual'][N-delta:]
return seq, qual, N-delta
if __name__ == "__main__":
from miscBowTie import BowTieReader, BowTieWriter
from cPickle import *
from optparse import OptionParser
parser = OptionParser()
parser.add_option("--input", dest="input", help="Input bowtie aligned file (gzipped)")
parser.add_option("--output", dest="output", help="Output composite read filename")
options, args = parser.parse_args()
reader = BowTieReader(options.input, is_paired=True)
print >> sys.stderr, "calculating base frequencies"
base_freq_pickle = options.input + ".base_freq.pickle"
if os.path.exists(base_freq_pickle):
base_freq = load(open(base_freq_pickle))
else:
base_freq = reader.get_base_frequency()
with open(options.input + ".base_freq.pickle", 'w') as f:
dump(base_freq, f)
print >> sys.stderr, "reading bowtie aligned file..."
writer = BowTieWriter(options.output)
for r1, r2 in reader:
seq, qual, overlap = compose2(r1, r2, base_freq)
writer.write_composite(r1, r2, seq, qual, overlap)
