Mercurial > repos > devteam > fastq_trimmer
annotate fastq_trimmer.py @ 2:fdff6f6a8763 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
| author | devteam |
|---|---|
| date | Fri, 18 Dec 2015 19:31:05 -0500 |
| parents | feb5479a48ff |
| children |
| rev | line source |
|---|---|
| 0 | 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 ) | |
|
2
fdff6f6a8763
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
0
diff
changeset
|
24 if right_column_offset != 0: |
| 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() |