Mercurial > repos > sanbi-uwc > assess_poliovirus_alignment
comparison assess_alignment.py @ 12:ee98dcd9aad4 draft
planemo upload for repository https://github.com/pvanheus/polio_report commit aa90f911e6269aba792c9814c98a659e631400b2-dirty
| author | sanbi-uwc |
|---|---|
| date | Tue, 27 Sep 2022 18:56:28 +0000 |
| parents | fff48fa8a22b |
| children | bf0bebcb6bb1 |
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| 11:fff48fa8a22b | 12:ee98dcd9aad4 |
|---|---|
| 163 parser.add_argument("--sample_name", help="Name of sample being analysed") | 163 parser.add_argument("--sample_name", help="Name of sample being analysed") |
| 164 parser.add_argument( | 164 parser.add_argument( |
| 165 "--dataset_names", type=comma_split, help="Comma separated names for datasets" | 165 "--dataset_names", type=comma_split, help="Comma separated names for datasets" |
| 166 ) | 166 ) |
| 167 parser.add_argument("--datasets", nargs="+") | 167 parser.add_argument("--datasets", nargs="+") |
| 168 parser.add_argument("--consensi", nargs="+") | |
| 169 args = parser.parse_args() | 168 args = parser.parse_args() |
| 170 | 169 |
| 171 offsets = { | 170 offsets = { |
| 172 # these are in 0-based coordinates, so off-by-one from NCBI 1-based coordinates | 171 # these are in 0-based coordinates, so off-by-one from NCBI 1-based coordinates |
| 173 "poliovirus1sabin": 2479, # V01150 | 172 "poliovirus1sabin": 2479, # V01150 |