alg = CompactAlignment()
alg.read_file_object(args.infile, args.informat)
# if args.actions:
# print >>sys.stderr, "will perform the following actions: %s" %",".join(args.actions)
# else:
# print >>sys.stderr, "No actions will be taken. Input in %s will be written to output in %s." %(args.informat,args.outformat)
if args.masksites:
alg.mask_gapy_sites(args.masksites)
if args.filterfragments:
rem = []
for k, v in alg.items():
if len(v.seq) < args.filterfragments:
rem.append(k)
for k in rem:
alg.pop(k, None)
if args.rename:
lines = [x for x in args.rename.readlines() if x != "\n"]
namemap = dict(
list(
zip((x.strip() for i, x in enumerate(lines) if i % 2 == 0),
(x.strip() for i, x in enumerate(lines) if i % 2 == 1))))
names = copy(list(alg.keys()))
for k in names:
alg[namemap[k]] = alg.pop(k)
alg.write(args.outfile, args.outformat)
args = parser.parse_args()
alg = CompactAlignment()
alg.read_file_object(args.infile,args.informat)
# if args.actions:
# print >>sys.stderr, "will perform the following actions: %s" %",".join(args.actions)
# else:
# print >>sys.stderr, "No actions will be taken. Input in %s will be written to output in %s." %(args.informat,args.outformat)
if args.masksites:
alg.mask_gapy_sites(args.masksites)
if args.filterfragments:
rem = []
for k, v in alg.iteritems():
if len(v.seq) < args.filterfragments:
rem.append(k)
for k in rem:
alg.pop(k, None)
if args.rename:
lines=filter(lambda x: x!="\n", args.rename.readlines())
namemap=dict(zip((x.strip() for i,x in enumerate(lines) if i%2 == 0),
(x.strip() for i,x in enumerate(lines) if i%2 == 1)))
names = copy(alg.keys())
for k in names:
alg[namemap[k]] = alg.pop(k)
alg.write(args.outfile, args.outformat)
