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") )
