args = parser.parse_args() if args.infile: asf = HiriseAssembly() asf.load_assembly(args.infile) # asf = HiriseAssembly() # asf.load_playout(args.infile) breaks=[] scores={} for l in open(args.breaks): if l[0]=="#": continue #Scaffold102239 741 1379 5097 -5.421961663655971 scaffold,a,b,slen,score = l.strip().split() a=int(a) #start b=int(b) #end # c=int(c) #lowpoint score=float(score) c=int((a+b)/2) breaks.append((scaffold,a,b,c)) scores[scaffold,a,b,c]=score # asf.add_breakpoints_ranges(breaks,debug=args.debug,scores=scores) asf.add_breakpoints_ranges(breaks,debug=args.debug) asf.validate() if args.outfile: asf.save_assembly( args.outfile )
# from __future__ import division from __future__ import print_function from builtins import range from past.utils import old_div from hirise_assembly import HiriseAssembly if __name__=="__main__": import sys import argparse parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('-d','--debug',default=False ,action="store_true",help="Turn on debugging ouput") parser.add_argument('-L','--layout',default=False ,help="A file containing a layout of contigs.") parser.add_argument('-i','--infile',default=False ,help="Filename for serialised assembly input file.") parser.add_argument('-o','--outfile',default=False,help="Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking.") args = parser.parse_args() if args.infile: asf = HiriseAssembly() asf.load_assembly(args.infile) if args.layout: asf.load_playout(args.layout) if args.outfile: asf.save_assembly( args.outfile )