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December 23, 2015 10:59
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split a fastq file into evenly size random chunks.
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""" | |
split a single fastq file in to random, non-overlapping subsets | |
arguments: | |
+ fastq file | |
+ number of splits | |
+ number of reps | |
e.g.: | |
python fq.split.py input.fastq 3 4 | |
will create 12 new files in 4 sets of 3. Each | |
set of 3 will contain all of the original records. | |
""" | |
import gzip | |
import random | |
from itertools import islice, izip | |
xopen = lambda fq: gzip.open(fq) if fq.endswith('.gz') else open(fq) | |
def fqiter(fq, n=4): | |
with xopen(fq) as fh: | |
fqclean = (x.strip("\r\n") for x in fh if x.strip()) | |
while True: | |
rec = [x for x in islice(fqclean, n)] | |
if not rec: raise StopIteration | |
assert all(rec) and len(rec) == 4 | |
yield rec | |
def fqsplit(fq, nchunks, nreps, prefix=None): | |
if prefix == None: prefix = fq + ".split" | |
prefix += "chunk-%i.rep-%i.fq" | |
fq_size = sum(1 for x in xopen(fq)) | |
assert fq_size % 4 == 0 | |
fq_size /= 4 # number of records | |
chunk_size = 1 + (fq_size) // nchunks | |
print >>sys.stderr, "chunk_size:", chunk_size | |
for rep in range(1, nreps + 1): | |
files = [open(prefix % (c, rep), 'w') for c in range(1, nchunks + 1)] | |
ints = range(fq_size) | |
random.shuffle(ints) | |
for i, fqr in izip(ints, fqiter(fq)): | |
chunk, chunk_i = divmod(i, chunk_size) | |
print >>files[chunk], "\n".join(fqr) | |
[f.close() for f in files] | |
if __name__ == "__main__": | |
import sys | |
fq = sys.argv[1] | |
nchunks = int(sys.argv[2]) | |
nreps = int(sys.argv[3]) | |
fqsplit(fq, nchunks, nreps) |
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Hi, I tried to use this script, but I got an error. The command I used is python fq.split.py. FTI.fastq 10 3.
I hope you can help. Thanks.
Hanghang