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https://github.com/galaxyproject/galaxy.git
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Daniel Blankenberg
8082c6f36f
Tools include: FASTQ Groomer convert between various FASTQ quality formats Combine FASTA and QUAL into FASTQ FASTQ joiner on paired end reads FASTQ splitter on joined paired end reads FASTQ to FASTA converter FASTQ Summary Statistics by column Filter FASTQ reads by quality score and length FASTQ Trimmer by column Manipulate FASTQ reads on various attributes Boxplot of quality statistics (Generic, with outliers)
38 lines
1.3 KiB
Python
38 lines
1.3 KiB
Python
#Dan Blankenberg
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import sys, os, shutil
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import imp
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from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
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def main():
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#Read command line arguments
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input_filename = sys.argv[1]
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script_filename = sys.argv[2]
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output_filename = sys.argv[3]
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additional_files_path = sys.argv[4]
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input_type = sys.argv[5] or 'sanger'
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#Save script file for debuging/verification info later
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os.mkdir( additional_files_path )
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shutil.copy( script_filename, os.path.join( additional_files_path, 'debug.txt' ) )
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fastq_manipulator = imp.load_module( 'fastq_manipulator', open( script_filename ), script_filename, ( '', 'r', imp.PY_SOURCE ) )
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out = fastqWriter( open( output_filename, 'wb' ), format = input_type )
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i = None
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reads_manipulated = 0
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for i, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
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new_read = fastq_manipulator.match_and_manipulate_read( fastq_read )
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if new_read:
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out.write( new_read )
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if new_read != fastq_read:
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reads_manipulated += 1
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out.close()
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if i is None:
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print "Your file contains no valid FASTQ reads."
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else:
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print 'Manipulated %s of %s reads (%.2f%%).' % ( reads_manipulated, i + 1, float( reads_manipulated ) / float( i + 1 ) * 100.0 )
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if __name__ == "__main__":
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main()
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