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comparison fastq_trimmer.py @ 0:0b9feb0ed628 draft

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Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:27:32 -0500
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-1:000000000000 0:0b9feb0ed628
1 #Dan Blankenberg
2 import sys
3 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
4
5 def main():
6 input_filename = sys.argv[1]
7 output_filename = sys.argv[2]
8 left_offset = sys.argv[3]
9 right_offset = sys.argv[4]
10 percent_offsets = sys.argv[5] == 'offsets_percent'
11 input_type = sys.argv[6] or 'sanger'
12 keep_zero_length = sys.argv[7] == 'keep_zero_length'
13
14 out = fastqWriter( open( output_filename, 'wb' ), format = input_type )
15 num_reads_excluded = 0
16 num_reads = None
17 for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
18 if percent_offsets:
19 left_column_offset = int( round( float( left_offset ) / 100.0 * float( len( fastq_read ) ) ) )
20 right_column_offset = int( round( float( right_offset ) / 100.0 * float( len( fastq_read ) ) ) )
21 else:
22 left_column_offset = int( left_offset )
23 right_column_offset = int( right_offset )
24 if right_column_offset > 0:
25 right_column_offset = -right_column_offset
26 else:
27 right_column_offset = None
28 fastq_read = fastq_read.slice( left_column_offset, right_column_offset )
29 if keep_zero_length or len( fastq_read ):
30 out.write( fastq_read )
31 else:
32 num_reads_excluded += 1
33 out.close()
34 if num_reads is None:
35 print "No valid fastq reads could be processed."
36 else:
37 print "%i fastq reads were processed." % ( num_reads + 1 )
38 if num_reads_excluded:
39 print "%i reads of zero length were excluded from the output." % num_reads_excluded
40
41 if __name__ == "__main__": main()