naobservatory / p2ra

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Add command list_taxids.py #213

Closed jeffkaufman closed 1 year ago

jeffkaufman commented 1 year ago

Example output:

taxid           filename        human_readable
10298           hsv_1           HSV-1
10310           hsv_2           HSV-2
10359           cmv             CMV
10376           ebv             EBV
10407           hbv             HBV
10566           hpv             HPV
10632           jcv             JCV
10804           aav2            AAV2
11103           hcv             HCV
11320           influenza       Influenza A
11520           influenza       Influenza B
11676           hiv             HIV
68558           aav6            AAV6
82300           aav5            AAV5
122928          norovirus       Norovirus (GI)
122929          norovirus       Norovirus (GII)
493803          mcv             MCV
1891762         bkv             BKV
2697049         sars_cov_2      SARS-COV-2

I realized I needed this in trying to check that all of our taxids are recognizeable by Kraken, because there wasn't previously an easy way to get the taxids.