2
83%
master: 83%

Ran 20 Oct 2019 10:04PM UTC

Files 21

Run time 1s

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Committed 20 Oct 2019 09:47PM UTC coverage: 79.389% (+0.02%) from 79.374%

Job # 708.2

Build Type

push

travis-ci

Committed by

iskandr

Commit Message

Add check .start_codon_complete (#230)

Using release 69 of Ensembl, I ran into an issue where some transcripts existed which had an annotated start_codon that only spanned two positions (example ENST00000543092).

Because of this, when .complete() was run, self.coding_sequence would hit an error when it tried to determine the _codon_positions:
ValueError: Expected 3 positions for start_codon of ENST00000543092 but got 2

It seems that more recent releases of Ensembl do not have this issue (they no longer list a start_codon for these cases).

To continue using Ensembl 69, I added the additional property .start_codon_complete which catches a _codon_position ValueError and returns False, and added self.start_codon_complete as an additional check in .complete().

Run Details

1248 of 1572 relevant lines covered (79.39%)

0.79 hits per line

openvax / pyensembl / 708 / 2
83%
master: 83%

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openvax / pyensembl / 708 / 2
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master: 83%

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