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 )
for tf,header in tfs_headers: orgfile.write("""* Break {label} \\includegraphics[width=70em]{{{pdffile}}} """.format(pdffile=tf,label=header).encode()) orgfile.flush() cmd = "emacs {} --batch -f org-export-as-pdf --kill ".format(orgfile.name) print(cmd) output,error = subprocess.Popen(shlex.split(cmd),stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr = subprocess.PIPE).communicate() if args.debug: print(output) print(error) of=re.sub(".org",".pdf",orgfile.name) cmd = "mv {} {}".format(of,args.report) output,error = subprocess.Popen(shlex.split(cmd),stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr = subprocess.PIPE).communicate() if args.debug: print(output) print(error) if args.outfile: asf.add_breakpoints_ranges(breaks,debug=args.debug,scores=scores,unlink_threshold=args.threshold, contig_break_threshold=args.contig_break_threshold,score_types=stype) asf.validate() asf.dump_layout( open(args.outfile,"wt") )