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1 #Dan Blankenberg
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2 import sys
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3 from galaxy_utils.sequence.fastq import fastqReader
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4
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5 def stop_err( msg ):
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6 sys.stderr.write( msg )
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7 sys.exit()
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8
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9 def main():
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10 if len(sys.argv) != 5:
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11 stop_err("Wrong number of arguments. Expect: fasta tabular desrc_split [type]")
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12 input_filename = sys.argv[1]
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13 output_filename = sys.argv[2]
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14 descr_split = int( sys.argv[3] ) - 1
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15 if descr_split < 0:
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16 stop_err("Bad description split value (should be 1 or more)")
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17 input_type = sys.argv[4] or 'sanger' #input type should ordinarily be unnecessary
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18
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19 num_reads = None
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20 fastq_read = None
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21 out = open( output_filename, 'wb' )
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22 if descr_split == 0:
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23 #Don't divide the description into multiple columns
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24 for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
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25 out.write( "%s\t%s\t%s\n" % ( fastq_read.identifier[1:].replace( '\t', ' ' ), fastq_read.sequence.replace( '\t', ' ' ), fastq_read.quality.replace( '\t', ' ' ) ) )
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26 else:
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27 for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
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28 words = fastq_read.identifier[1:].replace( '\t', ' ' ).split(None, descr_split)
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29 #pad with empty columns if required
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30 words += [""]*(descr_split-len(words))
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31 out.write( "%s\t%s\t%s\n" % ("\t".join(words), fastq_read.sequence.replace( '\t', ' ' ), fastq_read.quality.replace( '\t', ' ' ) ) )
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32 out.close()
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33 if num_reads is None:
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34 print "No valid FASTQ reads could be processed."
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35 else:
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36 print "%i FASTQ reads were converted to Tabular." % ( num_reads + 1 )
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37
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38 if __name__ == "__main__": main()
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