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[BUG] Mikado prepare forgets the phases of the CDS of input transcripts #133

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lucventurini opened this issue Oct 10, 2018 · 3 comments
Closed

[BUG] Mikado prepare forgets the phases of the CDS of input transcripts #133

lucventurini opened this issue Oct 10, 2018 · 3 comments
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@gemygk @lucventurini
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@lucventurini
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When a coding transcript with a truncated ORF at the 3', ie with a non-0 starting phase, passes through Mikado prepare, the program sets that phase to 0 arbitrarily. This should be repaired before the release is finalised.
@lucventurini lucventurini added this to the 1.3 milestone Oct 10, 2018
@lucventurini lucventurini changed the title [BUG] Mikado prepare forgets the [BUG] Mikado prepare forgets the phases of the CDS of input transcripts Oct 10, 2018
@lucventurini
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The problem stems from the fact that - stupidly - I am not storing the CDS phases in the load_into_storage function (Mikado.prepare.annotation_parser). This is the section that has to be fixed for mikado prepare to function properly.

lucventurini added a commit that referenced this issue Oct 10, 2018
@lucventurini
Fixed #133. Now implementing the unit-test
c4e30b5
lucventurini added a commit that referenced this issue Oct 10, 2018
@lucventurini
Implemented unit-test for #133
e492c10
@lucventurini
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Unit test added and all checks passed. Closing.

@lucventurini lucventurini reopened this Oct 12, 2018
lucventurini pushed a commit that referenced this issue Oct 12, 2018
Trying to fix an edge case for #133
45f06f4
lucventurini pushed a commit that referenced this issue Oct 12, 2018
Hopefully fix for #133
d381596
lucventurini pushed a commit that referenced this issue Oct 12, 2018
This should solve some corner cases for #133 (phase !=0 but first cod…
1d99d37 
…on is a valid start codon)
@lucventurini
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Solved the corner cases that were causing sparse failures. Closing for now, although we might want to give the option to adjust the start for CDSs (comparatively with what we do with TransDecoder) in the future.

@lucventurini lucventurini added this to Closed in Version 2 Oct 15, 2020
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Fixed EI-CoreBioinformatics#133. Now implementing the unit-test
6e7b941
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Implemented unit-test for EI-CoreBioinformatics#133
00b08e0
lucventurini pushed a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
Trying to fix an edge case for EI-CoreBioinformatics#133
ef388fc
lucventurini pushed a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
Hopefully fix for EI-CoreBioinformatics#133
89e4697
lucventurini pushed a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
This should solve some corner cases for EI-CoreBioinformatics#133 (ph…
0eedc59 
…ase !=0 but first codon is a valid start codon)
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