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1 #Dan Blankenberg
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2 import sys, os, shutil
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3 from galaxy_utils.sequence.fastq import fastqWriter, fastqSequencingRead, fastqCombiner, fastqFakeFastaScoreReader
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4 from galaxy_utils.sequence.fasta import fastaReader, fastaNamedReader
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5
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6 def main():
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7 #Read command line arguments
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8 fasta_filename = sys.argv[1]
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9 fasta_type = sys.argv[2] or 'fasta' #should always be fasta or csfasta? what if txt?
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10 qual_filename = sys.argv[3]
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11 qual_type = sys.argv[4] or 'qualsanger' #qual454 qualsolid
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12 output_filename = sys.argv[5]
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13 force_quality_encoding = sys.argv[6]
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14 if force_quality_encoding == 'None':
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15 force_quality_encoding = None
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16
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17 format = 'sanger'
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18 if fasta_type == 'csfasta' or qual_type == 'qualsolid':
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19 format = 'cssanger'
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20 elif qual_type == 'qualsolexa':
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21 format = 'solexa'
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22 elif qual_type == 'qualillumina':
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23 format = 'illumina'
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24
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25 out = fastqWriter( open( output_filename, 'wb' ), format = format, force_quality_encoding = force_quality_encoding )
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26 if qual_filename == 'None':
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27 qual_input = fastqFakeFastaScoreReader( format, quality_encoding = force_quality_encoding )
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28 else:
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29 qual_input = fastaNamedReader( open( qual_filename, 'rb' ) )
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30
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31 fastq_combiner = fastqCombiner( format )
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32 i = None
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33 skip_count = 0
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34 for i, sequence in enumerate( fastaReader( open( fasta_filename, 'rb' ) ) ):
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35 quality = qual_input.get( sequence )
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36 if quality:
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37 fastq_read = fastq_combiner.combine( sequence, quality )
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38 out.write( fastq_read )
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39 else:
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40 skip_count += 1
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41 out.close()
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42 if i is None:
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43 print "Your file contains no valid FASTA sequences."
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44 else:
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45 print qual_input.has_data()
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46 print 'Combined %s of %s sequences with quality scores (%.2f%%).' % ( i - skip_count + 1, i + 1, float( i - skip_count + 1 ) / float( i + 1 ) * 100.0 )
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47
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48 if __name__ == "__main__":
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49 main()
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