Ensembl / ensembl / 3850

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Remove X padding of 5' incomplete codon protein strings (#618)

* Remove phase retrieval and remove padding of mrna string

* Use start phase to accurately trim N-terminus of translation

* Remove debug print statements

* Restore N-padding of incomplete codon. Update translation code accordingly.

* Add in unit test for example transcript and associated data

* Remove debug comment

* Alter duplicate seq_region_name to fix broken old test

* Update gene count to 22

* Update gene count to 3

* Update expected transcript counts

* Update expected translation counts

* Update expected slice-related counts

* Update expected assert table counts

* Update expected counts

* Add analysis entry for new test data

* Update test to only take protein coding genes into account

* Remove old commented lines. Add description.

* Uncomment new test

23 of 23 new or added lines in 9 files covered. (100.0%)

32733 of 39823 relevant lines covered (82.2%)

821.9 hits per line