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openvax / pyensembl / 708
83%

Build:
DEFAULT BRANCH: master
Ran 20 Oct 2019 10:01PM UTC
Jobs 2
Files 21
Run time 3min
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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().

6 of 6 new or added lines in 1 file covered. (100.0%)

1247 of 1572 relevant lines covered (79.33%)

1.59 hits per line

Jobs
ID Job ID Ran Files Coverage
1 708.1 20 Oct 2019 10:01PM UTC 0
79.33
Travis Job 708.1
2 708.2 20 Oct 2019 10:04PM UTC 0
79.39
Travis Job 708.2
Source Files on build 708
Detailed source file information is not available for this build.
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