def downsample(f1, f2, data, N, quick=False):
""" get N random headers from a fastq file without reading the
whole thing into memory
modified from: http://www.biostars.org/p/6544/
quick=True will just grab the first N reads rather than do a true
downsampling
"""
if quick:
rand_records = range(N)
else:
records = sum(1 for _ in open(f1)) / 4
N = records if N > records else N
rand_records = sorted(random.sample(xrange(records), N))
fh1 = open_possible_gzip(f1)
fh2 = open_possible_gzip(f2) if f2 else None
outf1 = os.path.splitext(f1)[0] + ".subset" + os.path.splitext(f1)[1]
outf2 = os.path.splitext(f2)[0] + ".subset" + os.path.splitext(
f2)[1] if f2 else None
if utils.file_exists(outf1):
if not outf2:
return outf1, outf2
elif utils.file_exists(outf2):
return outf1, outf2
out_files = (outf1, outf2) if outf2 else (outf1)
with file_transaction(out_files) as tx_out_files:
if isinstance(tx_out_files, basestring):
tx_out_f1 = tx_out_files
else:
tx_out_f1, tx_out_f2 = tx_out_files
sub1 = open_possible_gzip(tx_out_f1, "w")
sub2 = open_possible_gzip(tx_out_f2, "w") if outf2 else None
rec_no = -1
for rr in rand_records:
while rec_no < rr:
rec_no += 1
for i in range(4):
fh1.readline()
if fh2:
for i in range(4):
fh2.readline()
for i in range(4):
sub1.write(fh1.readline())
if sub2:
sub2.write(fh2.readline())
rec_no += 1
fh1.close()
sub1.close()
if f2:
fh2.close()
sub2.close()
return outf1, outf2
def downsample(f1, f2, data, N, quick=False):
""" get N random headers from a fastq file without reading the
whole thing into memory
modified from: http://www.biostars.org/p/6544/
quick=True will just grab the first N reads rather than do a true
downsampling
"""
if quick:
rand_records = range(N)
else:
records = sum(1 for _ in open(f1)) / 4
N = records if N > records else N
rand_records = sorted(random.sample(xrange(records), N))
fh1 = open_possible_gzip(f1)
fh2 = open_possible_gzip(f2) if f2 else None
outf1 = os.path.splitext(f1)[0] + ".subset" + os.path.splitext(f1)[1]
outf2 = os.path.splitext(f2)[0] + ".subset" + os.path.splitext(f2)[1] if f2 else None
if utils.file_exists(outf1):
if not outf2:
return outf1, outf2
elif utils.file_exists(outf2):
return outf1, outf2
out_files = (outf1, outf2) if outf2 else (outf1)
with file_transaction(out_files) as tx_out_files:
if isinstance(tx_out_files, basestring):
tx_out_f1 = tx_out_files
else:
tx_out_f1, tx_out_f2 = tx_out_files
sub1 = open_possible_gzip(tx_out_f1, "w")
sub2 = open_possible_gzip(tx_out_f2, "w") if outf2 else None
rec_no = - 1
for rr in rand_records:
while rec_no < rr:
rec_no += 1
for i in range(4): fh1.readline()
if fh2:
for i in range(4): fh2.readline()
for i in range(4):
sub1.write(fh1.readline())
if sub2:
sub2.write(fh2.readline())
rec_no += 1
fh1.close()
sub1.close()
if f2:
fh2.close()
sub2.close()
return outf1, outf2