Adding subtyping option and fixes to -json

PoonLab / sierra-local

Retrieve HIVdb algorithm as XML and apply locally to HIV sequences

GNU General Public License v3.0

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Adding subtyping option and fixes to -json #86

Closed WilliamZekaiWang closed 1 year ago

GopiGugan commented 1 year ago

Running into an error with post-align:

Traceback (most recent call last):
  File "/usr/local/bin/postalign", line 8, in <module>
    sys.exit(cli())
  File "/home/vagrant/.local/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/vagrant/.local/lib/python3.10/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/vagrant/.local/lib/python3.10/site-packages/click/core.py", line 1675, in invoke
    sub_ctx = cmd.make_context(
  File "/home/vagrant/.local/lib/python3.10/site-packages/click/core.py", line 920, in make_context
    self.parse_args(ctx, args)
  File "/home/vagrant/.local/lib/python3.10/site-packages/click/core.py", line 1378, in parse_args
    value, args = param.handle_parse_result(ctx, opts, args)
  File "/home/vagrant/.local/lib/python3.10/site-packages/click/core.py", line 2360, in handle_parse_result
    value = self.process_value(ctx, value)
  File "/home/vagrant/.local/lib/python3.10/site-packages/click/core.py", line 2322, in process_value
    value = self.callback(ctx, self, value)
TypeError: Argument 'value' has incorrect type (expected list, got tuple)

Python version - 3.10.6 Cython - 0.29.32

ArtPoon commented 1 year ago

This seems to be a postalign issue. Please cross-post to that repo

WilliamZekaiWang commented 1 year ago

List of changes

Post-align is now the default alignment program
Added -subtype which allows users to call the subtyping.py script automatically
Added -alignment which allows users to specify choosing nuc-amino or post-align
Added new fields to the mutations
- isApobecMutation from file apobecs.csv
- isUnusual from file rx-all_subtype-all.csv
- primaryType from file mutation-type-pairs_hiv1.csv
- isSDRM from file sdrms_hiv1.csv
- hasStop and text fields
Added level field to drugScores
Added unittests

ArtPoon commented 1 year ago

Our best guess is that this is a dependency version issue with the postalign docker container. We might look into the click module for clues on the TypeError being raised. For now I think we might as well merge this PR because postalign is broken in master branch anyways.