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yatisht / usher

Ultrafast Sample Placement on Existing Trees
MIT License
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does `matUtils extract` has `-M` function? #376

Open liamxg opened 1 month ago

liamxg commented 1 month ago

Dear @yatisht,

I have find the in the webpage https://usher-wiki.readthedocs.io/en/latest/matUtils.html, it has -Mfunction, but when I typematUtils extract`, can not find this function: matUtils extract -i input.pb -a 5 -M my_metadata_1.tsv,my_metadata_2.tsv -k my_sample:25 -j my_sample_context.json

yatisht commented 1 month ago

I do see it:

> matUtils extract

extract options: -i [ --input-mat ] arg Input mutation-annotated tree file [REQUIRED] -g [ --input-gtf ] arg Input GTF annotations file (only used with --taxodium) -f [ --input-fasta ] arg Input FASTA reference file (only used with --taxodium) -s [ --samples ] arg Select samples by explicitly naming them. One per line -M [ --metadata ] arg Comma-delineated paths to metadata tsv/csvs containing categorical metadata values for a json or taxodium output. Used with -j and -l only -c [ --clade ] arg Select samples by membership in at least one of the indicated clade(s), comma delimited. ...

liamxg commented 1 month ago

Dear @yatisht, thanks. Is this the least version:

matUtils version
matUtils (v0.5.4)

yatisht commented 1 month ago

I am using v0.5.6.