collation module WIP #28
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ElDeveloper
requested changes
Oct 29, 2018
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@anupriyatripathi. This looks good. I only have two requests:
-
Remove the
collatefpfunction that exists in_fingerprint.pyand replace it for a function call to the newcollate_fingerprint function. This will avoid code replication. You should do the same for any tests that might be duplicated. -
Create a new semantic type for the CSI results. While you can process data directly from a filepath, it is recommended that all data coming into a QIIME2 plugin be imported into an Artifact. Let me know if you need help doing this.
Pull Request Test Coverage Report for Build 31
💛 - Coveralls |
ElDeveloper
approved these changes
Nov 1, 2018
| Returns | ||
| ------- | ||
| biom.Table | ||
| biom table containing mass-spec feature IDs (in rows) and molecular |
| ------- | ||
| biom.Table | ||
| biom table containing mass-spec feature IDs (in rows) and molecular | ||
| substructure IDs (in columns). Values are presence (1) or absence (0) |
| @@ -32,10 +32,10 @@ def test_siriusBinaryPath(self): | |||
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| def test_fingerprintOut(self): | |||
| with self.assertRaises(ValueError): | |||
| collatefp(self.emptycsi) | |||
| collate_fingerprint(self.emptycsi) | |||
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Can you delete this and the next testing method?
|
addressed :) |
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This PR adds a module to collate fingerprints if predicted by CSI:FingerID outside chemistree