[2] | 1 | #!/usr/bin/env python |
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| 2 | |
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| 3 | """ |
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| 4 | Split fixed length paired end reads |
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| 5 | """ |
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| 6 | |
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| 7 | import os, sys |
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| 8 | |
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| 9 | if __name__ == '__main__': |
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| 10 | |
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| 11 | infile = sys.argv[1] |
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| 12 | outfile_end1 = open(sys.argv[2], 'w') |
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| 13 | outfile_end2 = open(sys.argv[3], 'w') |
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| 14 | |
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| 15 | i = 0 |
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| 16 | |
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| 17 | for line in file( infile ): |
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| 18 | line = line.rstrip() |
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| 19 | |
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| 20 | if not line: |
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| 21 | continue |
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| 22 | |
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| 23 | end1 = '' |
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| 24 | end2 = '' |
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| 25 | |
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| 26 | line_index = i % 4 |
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| 27 | |
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| 28 | if line_index == 0: |
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| 29 | end1 = line + '/1' |
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| 30 | end2 = line + '/2' |
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| 31 | |
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| 32 | elif line_index == 1: |
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| 33 | seq_len = len(line)/2 |
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| 34 | end1 = line[0:seq_len] |
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| 35 | end2 = line[seq_len:] |
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| 36 | |
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| 37 | elif line_index == 2: |
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| 38 | end1 = line + '/1' |
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| 39 | end2 = line + '/2' |
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| 40 | |
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| 41 | else: |
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| 42 | qual_len = len(line)/2 |
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| 43 | end1 = line[0:qual_len] |
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| 44 | end2 = line[qual_len:] |
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| 45 | |
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| 46 | outfile_end1.write('%s\n' %(end1)) |
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| 47 | outfile_end2.write('%s\n' %(end2)) |
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| 48 | |
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| 49 | i += 1 |
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| 50 | |
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| 51 | if i % 4 != 0 : |
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| 52 | sys.stderr.write("WARNING: Number of lines in the input file was not divisible by 4.\nCheck consistency of the input fastq file.\n") |
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| 53 | outfile_end1.close() |
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| 54 | outfile_end2.close() |
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