Mercurial > repos > miller-lab > genome_diversity
comparison make_phylip.py @ 37:884ccb07885b
Fixed output_id
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Wed, 20 Nov 2013 16:43:43 -0500 |
| parents | 51cd0307fb70 |
| children |
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| 36:51cd0307fb70 | 37:884ccb07885b |
|---|---|
| 400 parser.add_argument('--chrClmn',metavar='int',type=int,help='the column with the chromosome.',required=True) | 400 parser.add_argument('--chrClmn',metavar='int',type=int,help='the column with the chromosome.',required=True) |
| 401 parser.add_argument('--posClmn',metavar='int',type=int,help='the column with the SNPs position.',required=True) | 401 parser.add_argument('--posClmn',metavar='int',type=int,help='the column with the SNPs position.',required=True) |
| 402 parser.add_argument('--refClmn',metavar='int',type=int,help='the column with the reference nucleotide.',required=True) | 402 parser.add_argument('--refClmn',metavar='int',type=int,help='the column with the reference nucleotide.',required=True) |
| 403 parser.add_argument('--altrClmn',metavar='int',type=int,help='the column with the derived nucleotide.',required=True) | 403 parser.add_argument('--altrClmn',metavar='int',type=int,help='the column with the derived nucleotide.',required=True) |
| 404 parser.add_argument('--output',metavar='output',type=str,help='the output',required=True) | 404 parser.add_argument('--output',metavar='output',type=str,help='the output',required=True) |
| 405 parser.add_argument('--output_id',metavar='int',type=int,help='the output id',required=True) | |
| 405 parser.add_argument('--gd_indivs',metavar='input gd_indivs file',type=str,help='the input reference species columns in the input file.',required=True) | 406 parser.add_argument('--gd_indivs',metavar='input gd_indivs file',type=str,help='the input reference species columns in the input file.',required=True) |
| 406 #~ | 407 #~ |
| 407 parser.add_argument('--inputCover',metavar='input gd_snp cover file',type=str,help='the input file with the table in gd_snp/gd_genotype cover format.',required=False,default=False) | 408 parser.add_argument('--inputCover',metavar='input gd_snp cover file',type=str,help='the input file with the table in gd_snp/gd_genotype cover format.',required=False,default=False) |
| 408 parser.add_argument('--inputCover_type',metavar='input cover type',type=str,help='the cover input file type (gd_snp or gd_genotype)',required=False,default=False) | 409 parser.add_argument('--inputCover_type',metavar='input cover type',type=str,help='the cover input file type (gd_snp or gd_genotype)',required=False,default=False) |
| 409 parser.add_argument('--gd_indivs_cover',metavar='input gd_indivs file',type=str,help='the input reference species columns in the input cover file.',required=False,default=False) | 410 parser.add_argument('--gd_indivs_cover',metavar='input gd_indivs file',type=str,help='the input reference species columns in the input cover file.',required=False,default=False) |
| 429 args = parser.parse_args() | 430 args = parser.parse_args() |
| 430 | 431 |
| 431 inSNPf = args.input | 432 inSNPf = args.input |
| 432 inSNPf_type = args.input_type | 433 inSNPf_type = args.input_type |
| 433 outfile = args.output | 434 outfile = args.output |
| 435 outfile_id = args.output_id | |
| 434 gd_indivs = args.gd_indivs | 436 gd_indivs = args.gd_indivs |
| 435 pxchrx = args.chrClmn | 437 pxchrx = args.chrClmn |
| 436 pxpos = args.posClmn | 438 pxpos = args.posClmn |
| 437 pxntA = args.refClmn | 439 pxntA = args.refClmn |
| 438 pxntB = args.altrClmn | 440 pxntB = args.altrClmn |