Better handling of separator directives and feature selection #75
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standage
commented
Jun 27, 2019
| @@ -53,4 +53,5 @@ def main(args): | |||
| ) | |||
| evalstream = tag.bae.eval_stream(locusstream) | |||
| writer = tag.writer.GFF3Writer(evalstream, args.out) | |||
| writer.complex_separators = False | |||
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Here, we want separators to mark boundaries between loci, not between features within a locus.
| @@ -58,4 +58,5 @@ def main(args): | |||
| minperc=args.min_perc | |||
| ) | |||
| writer = tag.writer.GFF3Writer(locusstream, args.out) | |||
| writer.complex_separators = False | |||
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Here, we want separators to mark boundaries between loci, not between features within a locus.
| @@ -103,8 +103,6 @@ def __repr__(self): | |||
| if string != '': | |||
| string += '\n' | |||
| string += str(feature) | |||
| if self.is_complex: | |||
| string += '\n###' | |||
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This is now delegated to the GFF3 writer.
Codecov Report
@@ Coverage Diff @@
## master #75 +/- ##
=====================================
Coverage 100% 100%
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Files 23 23
Lines 1269 1278 +9
Branches 290 292 +2
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+ Hits 1269 1278 +9
Continue to review full report at Codecov.
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This update mashes together two changes. First, it gives finer control to how and when separator directives are printed after complex features. Second, it enables selection of multiple feature types simultaneously in the
tag.select.featuresfunction and updates thebaemodule to correctly use this function intraversemode.API documentation up-to-date? Docstring examples?