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Implemented comparison on Locus objects #216

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merged 5 commits into from
Nov 8, 2018
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iskandr
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@iskandr iskandr commented Oct 29, 2018

'gene.exonsdoes not work on Py3 (https://github.com/openvax/pyensembl/issues/215) due to lack of comparison forsorted`, fixing this by implementing basic comparison methods on Locus (base class for Exon).

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Travis failure:

FAIL: test_transcript_start_codon : Check that fields Transcript
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/miniconda/envs/test-environment-/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/travis/build/openvax/pyensembl/test/test_transcript_objects.py", line 31, in test_transcript_start_codon
    CTNNBIP1_004_locus, Locus.__str__(CTNNBIP1_004_transcript))
AssertionError: Expected locus Locus(contig=1, start=9850659, end=9878176, strand=-) but got Locus(contig=1, start=9850659, end=9878176, strand=-)

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(See Travis failure)

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coveralls commented Nov 2, 2018

Coverage Status

Coverage decreased (-0.4%) to 79.936% when pulling f11718b on comparison-on-Locus into 6329a03 on master.

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iskandr commented Nov 2, 2018

Standardized magic methods (including __str__) for Exon, Locus, Transcript, Gene objects, added unit tests for __str__.

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iskandr commented Nov 7, 2018

@julia326 OK to merge?

@iskandr iskandr merged commit 94ee900 into master Nov 8, 2018
@iskandr iskandr deleted the comparison-on-Locus branch November 8, 2018 17:38
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3 participants