def describe_fastq(filename):
if preprocess_radtag_lane.smartopen(filename).read(1) == '@':
lnum = 4
else:
lnum = 1
baseQ = None
fh = preprocess_radtag_lane.smartopen(filename)
while baseQ is None:
n,s,q = preprocess_radtag_lane.next_read_from_fh(fh)
baseQ = preprocess_radtag_lane.get_baseQ(q)
fh.close()
return lnum,baseQ
import os,sys,numpy
def describe_fastq(filename):
if preprocess_radtag_lane.smartopen(filename).read(1) == '@':
lnum = 4
else:
lnum = 1
baseQ = None
fh = preprocess_radtag_lane.smartopen(filename)
while baseQ is None:
n,s,q = preprocess_radtag_lane.next_read_from_fh(fh)
baseQ = preprocess_radtag_lane.get_baseQ(q)
fh.close()
return lnum,baseQ
fname,qualcut = sys.argv[1:]
qualcut = float(qualcut)
lnum,baseQ = describe_fastq(fname)
fh = preprocess_radtag_lane.smartopen(fname)
while 1:
n,s,qs = preprocess_radtag_lane.next_read_from_fh(fh,lnum)
if len(n) == 0: break
qa = numpy.array([ord(c) - baseQ for c in qs])
if qa.mean() >= qualcut:
print preprocess_radtag_lane.as_fq_line(n,s,qa,baseQ,lnum),
#!/usr/bin/env python
import os, sys
from radtag_denovo import preprocess_radtag_lane
infile, outfile = sys.argv[1:]
if not os.path.exists(os.path.dirname(outfile)):
os.makedirs(os.path.dirname(outfile))
ifh = preprocess_radtag_lane.smartopen(infile)
ofh = preprocess_radtag_lane.smartopen(outfile, "w")
r = preprocess_radtag_lane.next_read_from_fh(ifh)
while r[0]:
r[0] = "%s %s:%s" % (tuple(r[0].rsplit(":", 2)))
ofh.write(preprocess_radtag_lane.as_fq4_lines(*r))
r = preprocess_radtag_lane.next_read_from_fh(ifh)
ifh.close()
ofh.close()
