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Back translate #74
Back translate #74
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Note that I use the NM to NP lookup table form the |
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I rebased and squashed this branch on current master, makes reviewing easier. |
I'm wondering a bit about naming, i.e.,:
And in code:
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# TODO: | ||
# - Support reference sequences other than transcript or protein. | ||
# - Check input: | ||
# - without_dna: Does the reference amino acid fit? |
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I don't understand this. Is this a TODO before we can merge this?
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No, I don't think this is blocking.
- Currently the back translator only supports NM or NP. In principle other references (NG, NC, LGC, ENSx) can also work.
- This refers to the name checker. We currently do not check whether the reference amino acid is actually there. E.g., for
p.Glu1Arg
we do not check whether there is a glutamine at position 1.
@jfjlaros I revised this PR and fixed most of the issues I could find. I just commented with some small remaining questions. Before merging this I would also like to include some tests. |
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From an It still sort of works, since the NCBI will now be queried, but of course we would like to use the cached I think we should first fix the database to store the versions separately. Note that this is only picked up by the unit tests when disabling the internet connection. |
After some tests it looks like we can actually have transcript-protein links with version numbers, so we should probably do that first. |
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Added back translate interface.