[2] | 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 | from galaxy_utils.sequence.fasta import fastaWriter |
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| 5 | |
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| 6 | def main(): |
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| 7 | input_filename = sys.argv[1] |
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| 8 | output_filename = sys.argv[2] |
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| 9 | input_type = sys.argv[3] or 'sanger' #input type should ordinarily be unnecessary |
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| 10 | |
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| 11 | num_reads = None |
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| 12 | fastq_read = None |
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| 13 | out = fastaWriter( open( output_filename, 'wb' ) ) |
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| 14 | for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): |
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| 15 | out.write( fastq_read ) |
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| 16 | out.close() |
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| 17 | if num_reads is None: |
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| 18 | print "No valid FASTQ reads could be processed." |
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| 19 | else: |
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| 20 | print "%i FASTQ reads were converted to FASTA." % ( num_reads + 1 ) |
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| 21 | |
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| 22 | if __name__ == "__main__": main() |
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