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Transcript.coding_sequence didn't work for non-coding transcripts #136

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merged 2 commits into from
Feb 23, 2016

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iskandr
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@iskandr iskandr commented Feb 23, 2016

  • Transcript.coding_sequence should return None rather than trying to slice into an empty Transcript.sequence
  • It was impossible to look up sequences in Ensembl 83 since they added a version number to every FASTA key (added a test for this)

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# .e.g.
# "ENST00000448914.1" instead of "ENST00000448914"
# So now we have to parse out the identifier
seq_id = seq_entry.metadata["id"].split(".")[0]
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Can you add a test that would break if you didn't have this?

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I did, check out test_transcript_sequence_ensembl83

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Oops, somehow didn't think that would cover it, cool

@tavinathanson
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LGTM

iskandr added a commit that referenced this pull request Feb 23, 2016
Transcript.coding_sequence didn't work for non-coding transcripts
@iskandr iskandr merged commit e9ec65a into master Feb 23, 2016
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2 participants