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#!/usr/bin/env python
from __future__ import print_function
import os, sys, argparse
def eprint(*args, **kwargs):
print(*args, file=sys.stderr, **kwargs)
#*******************************************************************************
def parse_file(file_name, read_set):
line_id = 0
name = ''
data = ''
qual = ''
valid = False
with (open(file_name)) as f:
for line in f:
if (line_id == 0):
if (valid):
if (len(name) == 0 or len(data) == 0 or len(data) != len(qual)):
eprint('File is not in FASTQ format')
sys.exit(1)
valid = False
if (name in read_set):
print(name + '2')
else:
read_set.add(name)
print(name + '1')
print(data)
print('+')
print(qual)
name = line.rstrip().split(' ')[0]
data = ''
qual = ''
line_id = 1
elif (line_id == 1):
if (line[0] == '+'):
line_id = 2
else:
data += line.rstrip()
elif (line_id == 2):
qual += line.rstrip()
if (len(qual) >= len(data)):
valid = True
line_id = 0
if (valid):
if (len(name) == 0 or len(data) == 0 or len(data) != len(qual)):
eprint(len(name), len(data), len(qual))
eprint('File is not in FASTQ format')
sys.exit(1)
if (name in read_set):
print(name + '2')
else:
read_set.add(name)
print(name + '1')
print(data)
print('+')
print(qual)
#*******************************************************************************
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='''Script for preprocessing
Illumina paired-end reads for usage in Racon. Each read will get unique
header up to the first white space to distinguish those forming a pair.''')
parser.add_argument('first', help='''File containing the first read of a pair
or both.''')
parser.add_argument('second', nargs='?', help='''Optional file containing
read pairs of the same paired-end sequencing run.''')
args = parser.parse_args()
read_set = set()
parse_file(args.first, read_set)
if (args.second is not None):
parse_file(args.second, read_set)
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