Comments (3)
jsaquing
commented on August 17, 2024
I've seen this bug come up in some of the PacBio data. Could you list some specific examples?
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bj8th
commented on August 17, 2024
@jsaquing I do not have one handy right now. To find an example you can call db_session.query(Transcript).all()
then for each transcript call transcript.orfs[0]
Doing this would eventually find a bug.
You can also write some unit tests to check the ORF start and stop for + and - strands
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bj8th
commented on August 17, 2024
Transcripts that exhibit bug:
ERROR:root:Bad Transcript ENST00000316485.11
ERROR:root:Bad Transcript ENST00000378125.4
ERROR:root:Bad Transcript ENST00000396846.8
ERROR:root:Bad Transcript ENST00000429238.2
ERROR:root:Bad Transcript ENST00000452392.2
ERROR:root:Bad Transcript ENST00000494651.7
ERROR:root:Bad Transcript ENST00000519718.1
ERROR:root:Bad Transcript ENST00000549499.1
ERROR:root:Bad Transcript ENST00000551025.4
ERROR:root:Bad Transcript ENST00000594769.5
ERROR:root:Bad Transcript ENST00000596400.1
ERROR:root:Bad Transcript ENST00000597658.1
ERROR:root:Bad Transcript ENST00000611392.5
ERROR:root:Bad Transcript ENST00000618573.4
ERROR:root:Bad Transcript ENST00000622608.1
ERROR:root:Bad Transcript ENST00000638375.1
ERROR:root:Bad Transcript ENST00000639222.1
ERROR:root:Bad Transcript ENST00000639419.1
ERROR:root:Bad Transcript ENST00000639615.1
ERROR:root:Bad Transcript ENST00000639793.1
ERROR:root:Bad Transcript ENST00000639929.1
ERROR:root:Bad Transcript ENST00000640103.1
ERROR:root:Bad Transcript ENST00000640432.1
ERROR:root:Bad Transcript ENST00000650585.1
ERROR:root:Bad Transcript ENST00000681176.1
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Related Issues (20)
- sQTL representations in biosurfer
- Associate novelty information for PacBio transcripts read into Biosurfer
- Gene-row track for expression visualization
- Display "absolute" frame of translation instead of relative HOT 1
- EXITC detection raises error when aligning some transcripts
- Implement generic ProteinFeature class
- ProteinAlignmentBlock should account for AA sequence matches HOT 1
- Refactor Exon to map against an association table between the transcript and exon tables HOT 2
- Resolving overlaps between domain mappings HOT 2
- Refactoring/optimization of IsoformPlot HOT 1
- Reference database initialization
- How to better organize different data sources
- Abstract data structure to handle relationships among parent and children
- Behavior of linking Nucleotides to Residues is possibly counterintuitive
- Annotation primitives as objects themselves HOT 2
- Wiki for Biosurfer Project HOT 1
- Clean up imports and standardize how code accesses resources within project directory
- Frameshifts are reversed for minus strand genes
- initial database creation
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