Mercurial > repos > devteam > fastq_manipulation
comparison fastq_manipulation.py @ 0:5d1e9e13e8db draft
Imported from capsule None
| author | devteam |
|---|---|
| date | Mon, 27 Jan 2014 09:26:01 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:5d1e9e13e8db |
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| 1 #Dan Blankenberg | |
| 2 import sys, os, shutil | |
| 3 import imp | |
| 4 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter | |
| 5 | |
| 6 def main(): | |
| 7 #Read command line arguments | |
| 8 input_filename = sys.argv[1] | |
| 9 script_filename = sys.argv[2] | |
| 10 output_filename = sys.argv[3] | |
| 11 additional_files_path = sys.argv[4] | |
| 12 input_type = sys.argv[5] or 'sanger' | |
| 13 | |
| 14 #Save script file for debuging/verification info later | |
| 15 os.mkdir( additional_files_path ) | |
| 16 shutil.copy( script_filename, os.path.join( additional_files_path, 'debug.txt' ) ) | |
| 17 | |
| 18 fastq_manipulator = imp.load_module( 'fastq_manipulator', open( script_filename ), script_filename, ( '', 'r', imp.PY_SOURCE ) ) | |
| 19 | |
| 20 out = fastqWriter( open( output_filename, 'wb' ), format = input_type ) | |
| 21 | |
| 22 i = None | |
| 23 reads_manipulated = 0 | |
| 24 for i, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): | |
| 25 new_read = fastq_manipulator.match_and_manipulate_read( fastq_read ) | |
| 26 if new_read: | |
| 27 out.write( new_read ) | |
| 28 if new_read != fastq_read: | |
| 29 reads_manipulated += 1 | |
| 30 out.close() | |
| 31 if i is None: | |
| 32 print "Your file contains no valid FASTQ reads." | |
| 33 else: | |
| 34 print 'Manipulated %s of %s reads (%.2f%%).' % ( reads_manipulated, i + 1, float( reads_manipulated ) / float( i + 1 ) * 100.0 ) | |
| 35 | |
| 36 if __name__ == "__main__": | |
| 37 main() |