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SplitSeqFile.py
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SplitSeqFile.py
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import sys
import os
import regex
from math import log10
from multiprocessing import Pool, cpu_count
import gzip
import struct
PROG_GUNZIP = "unpigz"
PROG_SPLIT = "gsplit"
PROG_GZIP = "pigz"
def _split_and_compress_fastq(fastq_fn, run_dir, split_prefix, split_lines, suffix_length):
ret = os.system("%s --stdout %s | %s --numeric-suffixes=1 --suffix-length=%d -l %d --filter='%s > $FILE.fq.gz' - %s" % \
(PROG_GUNZIP,
fastq_fn,
PROG_SPLIT,
suffix_length,
split_lines,
PROG_GZIP,
run_dir + '/' + split_prefix))
if ret != 0:
return None
else:
fn_pattern = regex.compile(regex.escape(split_prefix) + "([0-9]{" + str(suffix_length) + "})\.fq\.gz")
fn_matches = []
for fn in os.listdir(run_dir):
m = fn_pattern.match(fn)
if m:
fn_matches.append(m[1])
fn_matches = sorted(fn_matches, key = lambda x: int(x))
return [run_dir + '/' + split_prefix + fn_num + ".fq.gz" for fn_num in fn_matches]
def split_and_compress_fastq(run_dir, fastq_read1, fastq_read2, tag):
if not os.path.isdir(run_dir):
os.mkdir(run_dir)
split_reads = 1000000
split_lines = 4 * split_reads
suffix_length = 4
fn1 = _split_and_compress_fastq(fastq_read1, run_dir, tag+"1_", split_lines, suffix_length)
fn2 = _split_and_compress_fastq(fastq_read2, run_dir, tag+"2_", split_lines, suffix_length)
if __name__ == "__main__":
run_dir = sys.argv[1]
fastq_read1 = sys.argv[2]
fastq_read2 = sys.argv[3]
tag = sys.argv[4]
reads_list = split_and_compress_fastq(run_dir, fastq_read1, fastq_read2, tag)