Mercurial > repos > xuebing > sharplabtool
comparison tools/fastq/fastq_paired_end_interlacer.py @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
comparison
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 #Florent Angly | |
| 2 import sys | |
| 3 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqNamedReader, fastqJoiner | |
| 4 | |
| 5 def main(): | |
| 6 mate1_filename = sys.argv[1] | |
| 7 mate1_type = sys.argv[2] or 'sanger' | |
| 8 mate2_filename = sys.argv[3] | |
| 9 mate2_type = sys.argv[4] or 'sanger' | |
| 10 outfile_pairs = sys.argv[5] | |
| 11 outfile_singles = sys.argv[6] | |
| 12 | |
| 13 if mate1_type != mate2_type: | |
| 14 print "WARNING: You are trying to interlace files of two different types: %s and %s." % ( mate1_type, mate2_type ) | |
| 15 return | |
| 16 | |
| 17 type = mate1_type | |
| 18 joiner = fastqJoiner( type ) | |
| 19 out_pairs = fastqWriter( open( outfile_pairs, 'wb' ), format = type ) | |
| 20 out_singles = fastqWriter( open( outfile_singles, 'wb' ), format = type ) | |
| 21 | |
| 22 # Pairs + singles present in mate1 | |
| 23 nof_singles = 0 | |
| 24 nof_pairs = 0 | |
| 25 mate2_input = fastqNamedReader( open( mate2_filename, 'rb' ), format = type ) | |
| 26 i = None | |
| 27 for i, mate1 in enumerate( fastqReader( open( mate1_filename, 'rb' ), format = type ) ): | |
| 28 mate2 = mate2_input.get( joiner.get_paired_identifier( mate1 ) ) | |
| 29 if mate2: | |
| 30 out_pairs.write( mate1 ) | |
| 31 out_pairs.write( mate2 ) | |
| 32 nof_pairs += 1 | |
| 33 else: | |
| 34 out_singles.write( mate1 ) | |
| 35 nof_singles += 1 | |
| 36 | |
| 37 # Singles present in mate2 | |
| 38 mate1_input = fastqNamedReader( open( mate1_filename, 'rb' ), format = type ) | |
| 39 j = None | |
| 40 for j, mate2 in enumerate( fastqReader( open( mate2_filename, 'rb' ), format = type ) ): | |
| 41 mate1 = mate1_input.get( joiner.get_paired_identifier( mate2 ) ) | |
| 42 if not mate1: | |
| 43 out_singles.write( mate2 ) | |
| 44 nof_singles += 1 | |
| 45 | |
| 46 if (i is None) and (j is None): | |
| 47 print "Your input files contained no valid FASTQ sequences." | |
| 48 else: | |
| 49 print 'There were %s single reads.' % ( nof_singles ) | |
| 50 print 'Interlaced %s pairs of sequences.' % ( nof_pairs ) | |
| 51 | |
| 52 mate1_input.close() | |
| 53 mate2_input.close() | |
| 54 out_pairs.close() | |
| 55 out_singles.close() | |
| 56 | |
| 57 | |
| 58 if __name__ == "__main__": | |
| 59 main() |