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root/gclib/tophat_cpp/sra_to_solid.py
Revision: 29
Committed: Tue Aug 2 21:24:54 2011 UTC (8 years, 2 months 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;

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