ENH: Allow /dev/stdin as input alignment arg

neherlab / treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

MIT License

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ENH: Allow /dev/stdin as input alignment arg #241

Open corneliusroemer opened 1 year ago

corneliusroemer commented 1 year ago

To be able to work with compressed alignments, which is useful e.g. for monkeypox, it would be nice if treetime could accept the string /dev/stdin for alignments. Right now, it seems that alignments must be real files (isfile):

https://github.com/neherlab/treetime/blob/23f935fb6be29864c788108d5ab9ab1fccb3823d/treetime/sequence_data.py#L149