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comparison tools/fastq/fastq_combiner.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #Dan Blankenberg
2 import sys, os, shutil
3 from galaxy_utils.sequence.fastq import fastqWriter, fastqSequencingRead, fastqCombiner, fastqFakeFastaScoreReader
4 from galaxy_utils.sequence.fasta import fastaReader, fastaNamedReader
5
6 def main():
7 #Read command line arguments
8 fasta_filename = sys.argv[1]
9 fasta_type = sys.argv[2] or 'fasta' #should always be fasta or csfasta? what if txt?
10 qual_filename = sys.argv[3]
11 qual_type = sys.argv[4] or 'qualsanger' #qual454 qualsolid
12 output_filename = sys.argv[5]
13 force_quality_encoding = sys.argv[6]
14 if force_quality_encoding == 'None':
15 force_quality_encoding = None
16
17 format = 'sanger'
18 if fasta_type == 'csfasta' or qual_type == 'qualsolid':
19 format = 'cssanger'
20 elif qual_type == 'qualsolexa':
21 format = 'solexa'
22 elif qual_type == 'qualillumina':
23 format = 'illumina'
24
25 out = fastqWriter( open( output_filename, 'wb' ), format = format, force_quality_encoding = force_quality_encoding )
26 if qual_filename == 'None':
27 qual_input = fastqFakeFastaScoreReader( format, quality_encoding = force_quality_encoding )
28 else:
29 qual_input = fastaNamedReader( open( qual_filename, 'rb' ) )
30
31 fastq_combiner = fastqCombiner( format )
32 i = None
33 skip_count = 0
34 for i, sequence in enumerate( fastaReader( open( fasta_filename, 'rb' ) ) ):
35 quality = qual_input.get( sequence )
36 if quality:
37 fastq_read = fastq_combiner.combine( sequence, quality )
38 out.write( fastq_read )
39 else:
40 skip_count += 1
41 out.close()
42 if i is None:
43 print "Your file contains no valid FASTA sequences."
44 else:
45 print qual_input.has_data()
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 )
47
48 if __name__ == "__main__":
49 main()