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23 lines
763 B
Python
23 lines
763 B
Python
#Dan Blankenberg
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import sys
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from galaxy_utils.sequence.fastq import fastqReader
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from galaxy_utils.sequence.fasta import fastaWriter
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def main():
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input_filename = sys.argv[1]
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output_filename = sys.argv[2]
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input_type = sys.argv[3] or 'sanger' #input type should ordinarily be unnecessary
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num_reads = None
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fastq_read = None
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out = fastaWriter( open( output_filename, 'wb' ) )
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for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
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out.write( fastq_read )
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out.close()
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if num_reads is None:
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print "No valid FASTQ reads could be processed."
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else:
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print "%i FASTQ reads were converted to FASTA." % ( num_reads + 1 )
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if __name__ == "__main__": main()
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