/usr/bin/sra_to_solid is in tophat 2.1.1+dfsg1-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | #!/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;
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