Adds support for compressed strain name files #730
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Thanks, @benjaminotter! There were a couple of subtle bugs that I noted in the comments below. I'll add fixes for these and push a rebased version of all changes into a single commit. Then I think we're good to merge.
augur/utils.py
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We need to delete this line, too, so we don't turn is_vcf into a context manager.
augur/utils.py
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| @@ -713,7 +703,7 @@ def read_strains(*files, comment_char="#"): | |||
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| strains = set() | |||
| for input_file in files: | |||
| with open(input_file, 'r', encoding='utf-8') as ifile: | |||
| with open_file(input_file, 'r', encoding='utf-8') as ifile: | |||
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We have to drop the encoding keyword argument here because xopen does not support this. This is more evidence in support of implementing our own compression backend.
Uses the new `open_file` from the `io` module to open strains files and thereby support compressed inputs. Removes the unused older `open_file` function in `utils.py`. Fixes #722
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Codecov Report
@@ Coverage Diff @@
## master #730 +/- ##
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+ Coverage 31.51% 31.53% +0.02%
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Files 41 41
Lines 5674 5666 -8
Branches 1373 1371 -2
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- Hits 1788 1787 -1
+ Misses 3812 3805 -7
Partials 74 74
Continue to review full report at Codecov.
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Description of proposed changes
Replaces the
opencall in theread_strainsfunction withaugur.io.open_fileto support compressed strain name files.Related issue(s)
Fixes #722
Testing
Tested with compressed
include.txtandexclude.txtfiles from the ncov workflow