Vv ensembl dev susmi #660
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Vv ensembl dev susmi #660
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…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
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…3 prime UTRs in uncertain positions for the LOVD paper
This is used internally for validation as well as when presenting VCF data to users.
We attempt to push gap variants both left and right when validating, this used to result in up to 50 separate SeqRepo seq fetch calls. This commit replaces this with 1 50 base SeqRepo call. In the cases where we trigger gap movement attempts but only attempt 1 move Micro-benchmarking puts the 50bp fetch at about 4% slower than the 1bp fetch, but this commit will at least nearly half the time spent in SeqRepo seq fetch calls in every other case. The net effect on our input tests is a ~22% decrease in time taken to run, so this is probably a net gain.
This reduces the calls to parse hgvs objects from strings in mappings, by using the existing versions, where they exist already. First pass for improving efficiency/performance of genomic to transcript and transcript to genome mappings.
This will allow us to simplify the logic where we use report_hgvs2vcf to generate output later.
We used to call report_hgvs2vcf once per valid mapping genome, this change reduces this to just once and simplifies the logic around the genomic variant mapping output at the same time. Normally this will half the number of report_hgvs2vcf calls.
This also includes features to use existing validated VCF data when provided.
Don't double validate the same variant when doing fallback for RSG mapping recovery during hgvs to vcf conversion.
This patch reduces parsing hgvs objects from text by creating them directly from the available parts, in the function of hgvs_to_delins_hgvs in hgvs_utils, by replacing the function of vcfcp_to_hgvsstr with an new function of vcfcp_to_hgvs_obj.
Add a new hgvs_delins_parts_to_hgvs_obj function and use it instead of parse for the hgvs delins creation inside hgvs_utils.py. This is particularly used in hgvs<->vcf functions.
Also update docs a bit.
This avoids going from object to text only to then go back to object output almost all the time, allowing us to skip the unnecessary parser step.
Upgrade delins creation in gapped_mapping.py by using helper functions to directly create delins hgvs objects, as opposed to parsing the objects from text, which has performance costs.
This function hgvs_obj_from_existing_edit, is intended for when we are re-creating a variant with a new location, but the same edit.
Reduce the re-parsing of variants into hgvs delins objects via strings in vvMixinConverters.py, use hgvs_delins_parts_to_hgvs_obj instead.
We need slightly different bracket handling on predicted proteins, and different handling on */Ter= too. This allows us to fix the issue centrally rather than re-applying the edits in multiple places.
As yet unused, needed for object handling of protein variant mappings.
Expanded repeat formatting needs to happen before the final hgvs string to hgvs object conversion step, move it in preparation for switching this conversion to happening only once, inside initial format conversion.
Input formatting that depends on having a text quibble from user input needs to be completed before we parse into a hgvs object. Prepare for centralising input parsing by moving this kind of formatting before the intended hgvs string->hgvs object parsing point (at the end of the initial_format_conversions function).
Methyl syntax handling needs to happen before the first conversion into a hgvs object as the parser does not currently handle it.
Harden some initial input handling functions to cope with objects instead of strings, and add improved type aware posedit parsing.
Add required variables to handle methylation to the VVPosEdit, as well as a simple PosEdit to VVPosEdit function.
Jfw reparse reduction
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@John-F-Wagstaff. The main part of this commit is handling variants like NW_011332691.1(NM_012234.6):c.335+1G>C. See issue #657.
This transcript is on the reverse strand and is working. I have added in some tests too.