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does matUtils extract has -M function? #376

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liamxg opened this issue May 21, 2024 · 3 comments
Open

does matUtils extract has -M function? #376

liamxg opened this issue May 21, 2024 · 3 comments

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@liamxg
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liamxg commented May 21, 2024

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
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yatisht commented May 22, 2024

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
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liamxg commented May 22, 2024

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

matUtils version
matUtils (v0.5.4)

@yatisht
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yatisht commented May 22, 2024

I am using v0.5.6.

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