/tools/fastq/fastq_paired_end_joiner.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 38 lines · 30 code · 6 blank · 2 comment · 9 complexity · 8e1a32d88a11f9075f4ef3a00fe37ff1 MD5 · raw file
- #Dan Blankenberg
- import sys, os, shutil
- from galaxy_utils.sequence.fastq import fastqReader, fastqNamedReader, fastqWriter, fastqJoiner
- def main():
- #Read command line arguments
- input1_filename = sys.argv[1]
- input1_type = sys.argv[2] or 'sanger'
- input2_filename = sys.argv[3]
- input2_type = sys.argv[4] or 'sanger'
- output_filename = sys.argv[5]
-
- if input1_type != input2_type:
- print "WARNING: You are trying to join files of two different types: %s and %s." % ( input1_type, input2_type )
-
- input2 = fastqNamedReader( open( input2_filename, 'rb' ), input2_type )
- joiner = fastqJoiner( input1_type )
- out = fastqWriter( open( output_filename, 'wb' ), format = input1_type )
-
- i = None
- skip_count = 0
- for i, fastq_read in enumerate( fastqReader( open( input1_filename, 'rb' ), format = input1_type ) ):
- identifier = joiner.get_paired_identifier( fastq_read )
- fastq_paired = input2.get( identifier )
- if fastq_paired is None:
- skip_count += 1
- else:
- out.write( joiner.join( fastq_read, fastq_paired ) )
- out.close()
-
- if i is None:
- print "Your file contains no valid FASTQ reads."
- else:
- print input2.has_data()
- print 'Joined %s of %s read pairs (%.2f%%).' % ( i - skip_count + 1, i + 1, float( i - skip_count + 1 ) / float( i + 1 ) * 100.0 )
- if __name__ == "__main__":
- main()