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comparison tools/fastq/fastq_manipulation.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
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()