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Vv ensembl dev susmi #615

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Peter-J-Freeman
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Peter J. Freeman and others added 30 commits July 7, 2022 09:34
Merge pull request #389 from openvar/update_to_vvta
9e0313e 
Update to vvta
@sbenny1230
Merge pull request #390 from openvar/vv_ensembl_develop_pete
caec3fc 
commits that tackle what I saw for issue #387. It seems the reuested …
@sbenny1230
Merge pull request #391 from openvar/vv_ensembl_develop_pete
7b77b02 
Remove bad return statement for issue https://github.com/openvar/vari…
@sbenny1230
Remove ensembl not supported msg
9e4525e
@sbenny1230
Add transcript set when searching options
2602240
@sbenny1230
Add alt_aln_method to all t_to_g methods
56ceeec
@sbenny1230
Add alt_aln_method when searching
af3eb12
@sbenny1230
Tidy up Mixin code
5ad1528
@sbenny1230
Merge pull request #394 from openvar/vv_ensembl_develop
76daf7b 
Vv ensembl develop
@sbenny1230
Optimise and fix search through options
2df0d59
@sbenny1230
Switch key order for postgres in config test
8d9a28a
@sbenny1230
Clean up ensembl url code
b4c9eeb
@sbenny1230
Sort grch37 and grch38 ensembl urls
2cdc808
@sbenny1230
Fix bug in ensembl test variant 2
d5b8cf0
@sbenny1230
Add ensembl urls to ensembl input test
b4cb8b1
@sbenny1230
Sort incorrect values in ensembl tests 4 and 5
8444080
@sbenny1230
Add alt_aln_method when getting hgvs_stash_t
f4fb451
@sbenny1230
Update wrong genome build error
692a5ac
@sbenny1230
Add ensembl test for wrong genome build
f5bf878
@sbenny1230
Pass in alt_aln_method to g_to_t methods
65ffe0c
@sbenny1230
Add specific wrong build msg for each build
d4713ca
@sbenny1230
Tidy up wrong build warning code
4849921
@sbenny1230
Include genome build in new version msg
1f2d93a
@sbenny1230
Merge pull request #400 from openvar/vv_ensembl_dev_s_working
40c6b49 
Vv ensembl dev s working
@sbenny1230
Delete MANUAL.md
334ecb8
@sbenny1230
Rename MANUAL_UPDATED.md to MANUAL.md
05cc65c
@sbenny1230
Tidy up config
1fa9306
@sbenny1230
Merge pull request #401 from openvar/vv_ensembl
d310056 
Vv ensembl
@sbenny1230
Hide warn for irrelevant transcripts
f11fe6e 
Hide more recent version and not part of genome build warnings for irrelevant transcripts
@sbenny1230
Change build to grch38 in ensembl tests
af1ffcc
John-F-Wagstaff and others added 30 commits March 2, 2025 21:21
@John-F-Wagstaff
Move abort for con type variants before parsing
d41d1f7
@John-F-Wagstaff
Return early and reduce indent on non c prot map
fc3e7f8
@John-F-Wagstaff
Exploit early return to reduce indent in prot map
26de224
@John-F-Wagstaff
Further use of returns to reduce indent in protmap
36c8476
@John-F-Wagstaff
Add VVPosEdit for output formatting tweaks
401e0fb 
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.
@John-F-Wagstaff
Add helper functions for hgvs obj protein handling
d38b52b 
As yet unused, needed for object handling of protein variant mappings.
@John-F-Wagstaff
Switch protein to use hgvs obj to avoid re-parsing
81551f9
@John-F-Wagstaff
Add test for RNA indel -> prot del case
5e3512b
@John-F-Wagstaff
Move expanded repeat formatting before obj convert
3c1ef7b 
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.
@John-F-Wagstaff
Move input formatting before object creation point
d79c2ed 
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).
@John-F-Wagstaff
Move methyl syntax suffix handling before obj conv
006c44c 
Methyl syntax handling needs to happen before the first conversion into
a hgvs object as the parser does not currently handle it.
@John-F-Wagstaff
Update/improve tests for variant format_quibble
ecb52c2
@John-F-Wagstaff
Reduce hgvs obj re-parsing in complex_descriptions
1a1b8e3
@John-F-Wagstaff
Slight output formatting improvement HGVS AA
a9e431c
@John-F-Wagstaff
Improve formatting hgvs output on prot/NA
a5d885b
@John-F-Wagstaff
Improve handling of bad mappings in gapped_mapping
b22dfdc
@John-F-Wagstaff
Fix handling of ref type/source with obj not str
731878f
@John-F-Wagstaff
Make refseq mistake finder work for txt *and* obj
bec39cf
@John-F-Wagstaff
Harden initial convert to obj presence + parser
8572b28 
Harden some initial input handling functions to cope with objects
instead of strings, and add improved type aware posedit parsing.
@John-F-Wagstaff
Handel t->c shift without declaring as a re-map
08e52c4
@John-F-Wagstaff
Harden against n variant issues in mapping
7a1326a
@John-F-Wagstaff
Add limited allele parser improvements
b797255
@John-F-Wagstaff
Fix use_checking to handle object quibble as well
a491a81
@John-F-Wagstaff
Reduce unneeded exon fetch and re-start in mappers
db70e6b
@John-F-Wagstaff
Switch to early (singular) hgvs str->object parse
85e9474
@John-F-Wagstaff
Add&use handing for checked variants resubmitted
1e5d669
@John-F-Wagstaff
Add methylation to VVPosEdit + PosEdit->VVPosEdit
1188b2a 
Add required variables to handle methylation to the VVPosEdit, as well
as a simple PosEdit to VVPosEdit function.
@John-F-Wagstaff
Switch from text to VVPosEdit for methylation out
b026ea2
@Peter-J-Freeman
Merge pull request #663 from openvar/JFW_reparse_reduction
ed9ed24 
Jfw reparse reduction
@Peter-J-Freeman
update tests where gene symbol HIF1A\-AS3 changed to HIF1A\-AS1
40e9f66
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3 participants
@Peter-J-Freeman @sbenny1230 @John-F-Wagstaff