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)
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)
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.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)