/tools/fastq/fastq_trimmer.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 41 lines · 37 code · 3 blank · 1 comment · 13 complexity · a13c4e0f582e56c1766d1aaf0d8a7990 MD5 · raw file
- #Dan Blankenberg
- import sys
- from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
- def main():
- input_filename = sys.argv[1]
- output_filename = sys.argv[2]
- left_offset = sys.argv[3]
- right_offset = sys.argv[4]
- percent_offsets = sys.argv[5] == 'offsets_percent'
- input_type = sys.argv[6] or 'sanger'
- keep_zero_length = sys.argv[7] == 'keep_zero_length'
-
- out = fastqWriter( open( output_filename, 'wb' ), format = input_type )
- num_reads_excluded = 0
- num_reads = None
- for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
- if percent_offsets:
- left_column_offset = int( round( float( left_offset ) / 100.0 * float( len( fastq_read ) ) ) )
- right_column_offset = int( round( float( right_offset ) / 100.0 * float( len( fastq_read ) ) ) )
- else:
- left_column_offset = int( left_offset )
- right_column_offset = int( right_offset )
- if right_column_offset > 0:
- right_column_offset = -right_column_offset
- else:
- right_column_offset = None
- fastq_read = fastq_read.slice( left_column_offset, right_column_offset )
- if keep_zero_length or len( fastq_read ):
- out.write( fastq_read )
- else:
- num_reads_excluded += 1
- out.close()
- if num_reads is None:
- print "No valid fastq reads could be processed."
- else:
- print "%i fastq reads were processed." % ( num_reads + 1 )
- if num_reads_excluded:
- print "%i reads of zero length were excluded from the output." % num_reads_excluded
- if __name__ == "__main__": main()