Fix chrM / MT normalization #226
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
julia326
approved these changes
Sep 5, 2019
| # standardize mitochondrial genome to be "MT" | ||
| if result == "M": | ||
| result = "MT" | ||
| if result.startswith("chr") and "_" not in result: |
There was a problem hiding this comment.
thought for the future: normalize_chromosome could be aware of its Pyensembl release and normalize it to that set of contig names?
There was a problem hiding this comment.
I was thinking something similar! It's a little tricky since the normalization also gets applied to GTF file contigs which are kind of a lower level concept but I suspect we could figure out a sane rewiring.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
In the dark ages of PyEnsembl we needed a quick way to annotate variants from hg19 and GRCh37 using Ensembl reference data. This lead to a dirty chromosome normalization hack where we turn e.g. "chr1" -> "1" and "chrM" -> "MT".
This was always a little questionable (since the mitochondrial sequences aren't actually the same) but even worse is incorrect for references like GRCh38.
So, this PR gets rid of two aspects of contig normaliztion: "chr" prefix is now preserved and we don't convert "M" -> "MT" for the mitochondrial genome.
Fixes: #225
To restore use of Ensembl data for hg19 variants we'll have to make a more local contig conversion option in Varcode.