refgenie / refgenconf

A Python object for standardized reference genome assets.
http://refgenie.databio.org
BSD 2-Clause "Simplified" License
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A list of seek keys #128

Closed nsheff closed 3 years ago

nsheff commented 3 years ago

I couldn't find it in the docs -- given a genome and asset, can I get a list of seek keys?

Really, what I want is to do something like:

seek_keys = rgc.get_seek_path_dict("hg38")

and then refer to the paths, now in dict form, like:

seek_keys.fasta.chrom_sizes
seek_keys.bowtie2_index.default

I can create something like this for default seek keys very easily like this:

ret = {}

g = "t7"
for a in rgc.list_assets_by_genome(g):
    ret[a] = rgc.seek(g, a, "default")

But I need this for all seek keys.

stolarczyk commented 3 years ago

Just added a method that will help: https://github.com/refgenie/refgenconf/pull/129/commits/3c8945eecc04ad6e25ece75844f15b7951d195ca

nsheff commented 3 years ago

awesome, that's all I needed!