gclib/tophat_cpp/sra_to_solid.py

#!/usr/bin/env python

"""
sra_to_solid.py
"""

import sys

use_message = '''
convert SOLiD sequences downloaded from SRA FTP (not via the web interface) to a format TopHat processes.
the script simply removes one primer quality value '!' from the sequences.

Usage:
    sra_to_solid input.fastq > output.fastq
'''

if __name__ == "__main__":
    if len(sys.argv) == 2:
        input_file = open(sys.argv[-1], 'r')
        expect_qual = 0
        for line in input_file:
            line = line.rstrip('\n')
            if expect_qual % 4  == 3:
                line = line[1:]
            
            print line
            expect_qual = (expect_qual + 1) % 4
                
    else:
        print use_message;
Revision:	29
Committed:	Tue Aug 2 21:24:54 2011 UTC (13 years, 1 month ago) by gpertea
File size:	716 byte(s)
Log Message:	adding tophat source work
Line	File contents
1	#!/usr/bin/env python
2
3	"""
4	sra_to_solid.py
5	"""
6
7	import sys
8
9	use_message = '''
10	convert SOLiD sequences downloaded from SRA FTP (not via the web interface) to a format TopHat processes.
11	the script simply removes one primer quality value '!' from the sequences.
12
13	Usage:
14	sra_to_solid input.fastq > output.fastq
15	'''
16
17	if __name__ == "__main__":
18	if len(sys.argv) == 2:
19	input_file = open(sys.argv[-1], 'r')
20	expect_qual = 0
21	for line in input_file:
22	line = line.rstrip('\n')
23	if expect_qual % 4 == 3:
24	line = line[1:]
25
26	print line
27	expect_qual = (expect_qual + 1) % 4
28
29	else:
30	print use_message;