import glob,os from fastq_reader import Fastq_Reader help_message = 'usage example: python check_hash_collisions.py -r 2 -i /project/home/hashed_reads/ -o /project/home/cluster_vectors/' if __name__ == "__main__": try: opts, args = getopt.getopt(sys.argv[1:],'hr:i:o:',["--filerank=","inputdir=","outputdir="]) except: print help_message sys.exit(2) for opt, arg in opts: if opt in ('-h','--help'): print help_message sys.exit() elif opt in ('-r',"--filerank"): fr = int(arg) elif opt in ('-i','--inputdir'): inputdir = arg if inputdir[-1] != '/': inputdir += '/' elif opt in ('-o','--outputdir'): outputdir = arg if outputdir[-1] != '/': outputdir += '/' hashobject = Fastq_Reader(inputdir,outputdir) HashFiles = glob.glob(os.path.join(hashobject.input_path,'*.hashq.*')) hashobject.infile = HashFiles[fr] t,n,H = hashobject.collision_report() print 'total hashed kmers:',t print 'total pairwise collisions:',n print 'collision histogram:',H
from fastq_reader import Fastq_Reader help_message = 'usage example: python check_hash_collisions.py -r 2 -i /project/home/hashed_reads/ -o /project/home/cluster_vectors/' if __name__ == "__main__": try: opts, args = getopt.getopt(sys.argv[1:], 'hr:i:o:', ["--filerank=", "inputdir=", "outputdir="]) except: print help_message sys.exit(2) for opt, arg in opts: if opt in ('-h', '--help'): print help_message sys.exit() elif opt in ('-r', "--filerank"): fr = int(arg) elif opt in ('-i', '--inputdir'): inputdir = arg if inputdir[-1] != '/': inputdir += '/' elif opt in ('-o', '--outputdir'): outputdir = arg if outputdir[-1] != '/': outputdir += '/' hashobject = Fastq_Reader(inputdir, outputdir) HashFiles = glob.glob(os.path.join(hashobject.input_path, '*.hashq.*')) hashobject.infile = HashFiles[fr] t, n, H = hashobject.collision_report() print 'total hashed kmers:', t print 'total pairwise collisions:', n print 'collision histogram:', H