biocore / scikit-bio / 3501
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Jobs 2
Files 79
Run time 36s
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wasade 
GFF3 IO (#1450)

* add GFF3 parser

* finish GFF3 reader/writer

* fix doctest and add gff3 to __init__

* add gff3 as default write format to IntervalMetadata

* fix pep8

* add more tests

* mv exception to the right place

* change gff3 parser API to take intervalmetadata

* parse the col 9 of attr in GFF3

* add writer template functions

fix readertests;
fix a bug in _yield_record

* write out the GFF3 writer.

other changes

* add escape translate

* fix bugs and add tests

* add roundtrip tests

* reorganize the code

* add _gff3_to_sequence/dna and their tests

* update doctest and docstring

* add reader/writer parameter doc

* add gff3 to sphinx doc build

* update changelog

* address comments

1. deleted docstring text copied from format spec.
2. changed API
3. added more tests

* fix pep8

* update API for generator

add doctest

* add more doctests and fix a bug

* fix pep8

* add unknown_seq_len to IntervalMetadata reader API

* update GFF3 APIs

* add a couple of more tests and doc

* mv print() to write()

fix a comment on arbitrary number in test

* fix comments on print/typo/doc language

add test case where seq id has a space

* fix 2 bugs

1. should return empty generator if reading an empty gff3 file
2. join the values if the attribute has multiple values

* add more tests

* add ``negate`` parameter to IntervalMetadata.drop

fix a few comments

* use the underlying functions to read fasta seq instead

9008 of 9069 relevant lines covered (99.33%)

1.99 hits per line

Uncovered Existing Lines

Lines Coverage ∆ File
1
100.0
 /home/travis/miniconda3/envs/env_name/lib/python3.5/site-packages/skbio/metadata/_interval.py
Jobs
ID Job ID Ran Files Coverage
1 3501.1 (PYTHON_VERSION=3.5 MAKE_DOC=TRUE) 0
99.33
 Travis Job 3501.1
2 3501.2 (PYTHON_VERSION=3.4 USE_CYTHON=TRUE) 0
99.33
 Travis Job 3501.2
Source Files on build 3501
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