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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() |
