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biocore / scikit-bio / 3630 / 1
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Ran 18 Apr 2018 09:05PM UTC
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18 Apr 2018 08:57PM UTC coverage: 99.261% (-0.05%) from 99.306%
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RNAer
Add embl support - References #1483 (#1495)

* DEV: prototype of embl formatter module

Add test and module for embl formatter object. Can build empty
document for embl. test fails.

* TST: working on base tests for embl modules

Implemented Sniffer and _parse_id (looks like to _parse_locus of
genbank module)

* TST: add tests and boilerplate functions

* DEV: parsing embl references

* DEV: working on embl sections

I'm trying to split embl records like genbank

* DEV: parsing embl sections (like sequences)

* DOC: changes in documentation - ID converted in LOCUS

Little chnages in documentation. Now ID is translated in LOCUS key

* MAINT: more comments - raising exceptions using uniprot records

* MAINT: passing tests and pyflake

Run `make test` and fix all issues

* TST: added new tests

Adding tests to deal with other embl sections

* DEV: dealing with feature table

* BUG: fixed bugs in embl.py and test_embl.py

* BUG: fixed bug in _parse_loc_str

Proposed as PR #1490, references #1489

* TST: added writer and roundtrip tests

* DEV: dealing with writer methods

Writing sequences and ID keys

* DEV: serializing reference and sources

* DEV: Serializing features - sorted feature in test files

During tests validation, I had to sort features alphabetically,
since serialize_single_feature sort feature metadata keys

* DEP: removed some deprecated methods

replaced pd.core.common.is_list_like with pd.api.types.is_list_like,
self.index.sym_diff with self.index.symmetric_difference and
self.assertRaisesRegexp with self.assertRaisesRegex

* TST: fixed test to deal with feature-level-products

feature-level-products are ENA entries which derive from others
entry (they could be Genes or RNA). Since features are related
to the parent entries, I can't read feature table and apply
it in a sequence that doesn't reflect the original annotations;
So, those records are treated like subsetting Se... (continued)

3954 of 4061 branches covered (97.37%)

9401 of 9471 relevant lines covered (99.26%)

0.99 hits per line

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