Adds --keeplength flag to maff-add action.
#84
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Hey @mikerobeson! It looks like some of the tests are now failing, should keeplength in the |
ebolyen
reviewed
Aug 22, 2024
| @@ -26,7 +26,8 @@ def run_command(cmd, output_fp, verbose=True): | |||
| subprocess.run(cmd, stdout=output_f, check=True) | |||
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| def _mafft(sequences_fp, alignment_fp, n_threads, parttree, addfragments): | |||
| def _mafft(sequences_fp, alignment_fp, n_threads, parttree, addfragments, | |||
| keeplength): | |||
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Suggested change
| keeplength): | |
| keeplength=False): |
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I left this as is for now as it is similar to addfragments. I just I just followed that lead of adding False in the mafft function. I can change that it that is the better way to go. :-)
ebolyen
reviewed
Aug 22, 2024
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@ebolyen, looks like the check pass now. :-) |
gregcaporaso
approved these changes
Sep 26, 2024
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Resolves #83
Allows an option to force the original alignment to keep it's original length while adding new sequences, as outlined here.
Users should keep in mind the following from the mafft docs (which is also in the plugin help text):