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1 #Dan Blankenberg
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2 import sys
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3
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4 def main():
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5 input_filename = sys.argv[1]
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6 output_filename = sys.argv[2]
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7 identifier_col = int( sys.argv[3] ) - 1
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8 sequence_col = int( sys.argv[4] ) - 1
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9 quality_col = int( sys.argv[5] ) - 1
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10
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11 max_col = max( identifier_col, sequence_col, quality_col )
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12 num_reads = None
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13 fastq_read = None
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14 skipped_lines = 0
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15 out = open( output_filename, 'wb' )
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16 for num_reads, line in enumerate( open( input_filename ) ):
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17 fields = line.rstrip( '\n\r' ).split( '\t' )
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18 if len( fields ) > max_col:
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19 out.write( "@%s\n%s\n+\n%s\n" % ( fields[identifier_col], fields[sequence_col], fields[quality_col] ) )
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20 else:
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21 skipped_lines += 1
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22
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23 out.close()
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24 if num_reads is None:
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25 print "Input was empty."
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26 else:
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27 print "%i tabular lines were written as FASTQ reads. Be sure to use the FASTQ Groomer tool on this output before further analysis." % ( num_reads + 1 - skipped_lines )
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28
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29 if __name__ == "__main__": main()
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