Centralize sequence read operations #1730
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #1730 +/- ##
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+ Coverage 72.94% 72.99% +0.05%
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Files 79 79
Lines 8317 8325 +8
Branches 1698 1698
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+ Hits 6067 6077 +10
+ Misses 1962 1960 -2
Partials 288 288 ☔ View full report in Codecov by Sentry. |
genehack
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The file reading is handled by augur.io.open_file, which is independent of Biopython.
These are more useful for type checking and rendering of documentation. I switched "Yields" to "Returns" to match the label of "Return type" in rendered docs.
The name clashes with augur.io.read_sequences which will be used in a future commit. This also presents the chance to add a short comment on the similarities and differences between the two functions.
This centralizes customization of the Biopython call. The 'format=' key is necessary for read_sequences - without it, the value is treated as a positional argument which is used by '*paths'.
This allows for centralized customization of the Biopython call.
This centralizes customization of the Biopython call. Added 'format=' key to improve readability.
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Description of proposed changes
General improvements before fixing CI failures related to sequence read.
Related issue(s)
#1727
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