Vv ensembl dev susmi #615
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Vv ensembl dev susmi #615
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Update to vvta
commits that tackle what I saw for issue #387. It seems the reuested …
Remove bad return statement for issue https://github.com/openvar/vari…
Vv ensembl develop
Vv ensembl dev s working
Vv ensembl
Hide more recent version and not part of genome build warnings for irrelevant transcripts
The underlying seq fetching code is 0 based but much of the overlying code in the expanded repeat handling acts as if it is 1 based, fix this.
This test set is conceptually the same as the existing C set, but twice as long and done with transcripts where there is a pair of n and c versions with the same within transcript sequence, and the same from transcript start coordinates, for the section in question. This allows us to test the offset c based coordinates against the more raw 1 based non offset n data. This test set also includes more n+offset type coordinates as opposed to the mainly n-offset in the original set along with more mutli-base repeats, which adds to the test coverage.
Both a few basic tests and a reverse genome -> transcript set, which is equivalent to a genomic version of those C tests with successful genomic mapping.
We used to need to check the transcript type, but we now handle all ref type within the expanded repeat code, so this feature is no longer used.
Although the variant position is still messed with we no longer convert the variant into a pseudo-g type and back when we get an intronic coordinate. This patch also cleans up the use of offset, without specifiers, in variable and function names, which is ambiguous. In the process we end up fixing a n type to c type coordinate conversion bug and preparing for addition of 3' UTR handling in the process.
intronic_or_utr would sometimes store the UTR status, but this was actually unused, instead it was mostly used to store the transcript when an intron was detected, as part of the handling for the now fixed abuse of the reference variable. The regular expression fixed missing bad characters in a repeat if one good repeat character was included.
Also tidy up some logic leftover from previous c<->n mapping methods now that we centralise it into separate functions. We also slightly adjust function naming and input logic from get_range_from_single to get_range_from_single_or_start to match actual usage.
Also adjust test for get_range_from_single_pos to match the new name of get_range_from_single_or_start_pos.
We do not use this function any more in the current usage pattern.
Also some use of startswith instead of re.match in ref type checking.
Updtes to the expanded repeat code for simple repeats only so far
Fix outstanding bugs
…iantValidator into vv_ensembl_dev_susmi
…e and intrins in r. descriptions as referred to in #545
…es2transcripts functionality
…680.6:c.153G>T in issue #651
…ing and HGNC genes with no transcript info openvar/rest_variantValidator#186 and also handle the longer deletions in #651
…nate alignments in patches vs the primary assembly. Issue #657
…3 prime UTRs in uncertain positions for the LOVD paper
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