/tools/fastq/fastq_paired_end_interlacer.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 59 lines · 47 code · 9 blank · 3 comment · 12 complexity · 33dd533483d53744a7b82af3d3bbd7db MD5 · raw file
- #Florent Angly
- import sys
- from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqNamedReader, fastqJoiner
- def main():
- mate1_filename = sys.argv[1]
- mate1_type = sys.argv[2] or 'sanger'
- mate2_filename = sys.argv[3]
- mate2_type = sys.argv[4] or 'sanger'
- outfile_pairs = sys.argv[5]
- outfile_singles = sys.argv[6]
- if mate1_type != mate2_type:
- print "WARNING: You are trying to interlace files of two different types: %s and %s." % ( mate1_type, mate2_type )
- return
- type = mate1_type
- joiner = fastqJoiner( type )
- out_pairs = fastqWriter( open( outfile_pairs, 'wb' ), format = type )
- out_singles = fastqWriter( open( outfile_singles, 'wb' ), format = type )
- # Pairs + singles present in mate1
- nof_singles = 0
- nof_pairs = 0
- mate2_input = fastqNamedReader( open( mate2_filename, 'rb' ), format = type )
- i = None
- for i, mate1 in enumerate( fastqReader( open( mate1_filename, 'rb' ), format = type ) ):
- mate2 = mate2_input.get( joiner.get_paired_identifier( mate1 ) )
- if mate2:
- out_pairs.write( mate1 )
- out_pairs.write( mate2 )
- nof_pairs += 1
- else:
- out_singles.write( mate1 )
- nof_singles += 1
- # Singles present in mate2
- mate1_input = fastqNamedReader( open( mate1_filename, 'rb' ), format = type )
- j = None
- for j, mate2 in enumerate( fastqReader( open( mate2_filename, 'rb' ), format = type ) ):
- mate1 = mate1_input.get( joiner.get_paired_identifier( mate2 ) )
- if not mate1:
- out_singles.write( mate2 )
- nof_singles += 1
- if (i is None) and (j is None):
- print "Your input files contained no valid FASTQ sequences."
- else:
- print 'There were %s single reads.' % ( nof_singles )
- print 'Interlaced %s pairs of sequences.' % ( nof_pairs )
- mate1_input.close()
- mate2_input.close()
- out_pairs.close()
- out_singles.close()
-
- if __name__ == "__main__":
- main()