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Update arsh4.files() to read from a datadir/meta.yaml file #2

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lianos opened this issue Apr 4, 2018 · 1 comment
Open

Update arsh4.files() to read from a datadir/meta.yaml file #2

lianos opened this issue Apr 4, 2018 · 1 comment
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@lianos
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lianos commented Apr 4, 2018

The names of the files in the archs4 datadir are hard coded in the archs4.files function.

As these files are updated from the ARCHS4 resource, their names will change. ie. the first mouse transcript-level hdf5 file was called "mouse_hiseq_eid_1.0.h5", but the second version is "mouse_hiseq_transcript_v2.h5".

In order to accommodate these changes, the datadir can have a meta.yaml file with a files section, which can look something like this:

files:
  mouse_transcript:
    filename: mouse_hiseq_transcript_v2.h5
    description: "mouse-level transcript quantitation downloaded on 3/3/2018"
  mouse_gene:
    filename: mouse_matrix.h5
    description: "mouse-level gene quantitation downloaded on ..."
  ...
@lianos lianos self-assigned this Apr 4, 2018
@tomsing1
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I just discovered Rstudio's config package. Might be useful for this, also allowing users to switch between different configuration profiles (defaults, dev, test, etc).

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