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Add helper class to streamline access to expressions and metadata #225
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Looks good in general, i have some smaller comments. Will try to play with it after lunch to see it in action :-)
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Looks good, I have a few additional small comments...
Please rebase to latest master to see if tests pass. You will probably see that you need to format your docstrings according to PEP8 and PEP257.
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Codecov Report
@@ Coverage Diff @@
## master #225 +/- ##
==========================================
+ Coverage 77.86% 80.72% +2.85%
==========================================
Files 25 27 +2
Lines 1455 1619 +164
==========================================
+ Hits 1133 1307 +174
+ Misses 322 312 -10
Continue to review full report at Codecov.
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@robertcv This looks good for MVP, please make linters happy to ensure that tests pass. Thanks for your contribution!
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def _get_gene_map(self, ensembl_ids: List[str]) -> dict: | ||
"""Fetch gene mapping from resolwe server.""" | ||
sublists = [ |
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return {
feature.feature_id: feature.name
for feature in self.resolwe.feature.filter(
feature_id__in=ensembl_ids,
species=self._table_samples[0].metadata["general"]["species"],
fields=["feature_id", "name"],
).iterate(CHUNK_SIZE)
}
This partially implements spec.
What is implemented:
ResolweBio
I usedCollectionTables
as this class functionality is, in a nutshell, exporting collections as tables of data