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Number MHCs#100

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ALGW71 wants to merge 23 commits intomainfrom
MHC
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Number MHCs#100
ALGW71 wants to merge 23 commits intomainfrom
MHC

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@ALGW71 ALGW71 commented Jun 25, 2025 •
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  • Provide new MHC model.
  • Account for gap between 100 and 1000 in the numbering.
  • Account for long sequences of 400.
  • There is a discrepancy between IMGT (French) and A-Nolan numbering for HLA-DRA.

ALGW71 and others added 23 commits May 1, 2025 16:15
@ALGW71
Add a flag for SCFV to the number method.
6b47f89
@ALGW71
Simple CWC fix for SCFVs.
940bfe9
@ALGW71
Trial code for new SCFV method, not reliant on CWC. Need to document …
8116ec5 
…and test.
@ALGW71
More edits and testing on multi chain fasta.
371c636
@ALGW71
SCFV code when missing CWC is as good as ever. Now add back in CWC an…
b741e58 
…d create a fallback.
@ALGW71
SCFV mode now working better - CWC does not work. Back to window method.
14d0ad7
@ALGW71
On test set 6/1133 are misnumbered but still ID as SCFVs.
f52c9fd
@ALGW71
Added comments for clarity.
aeed5d3
@ALGW71
Added comments for clarity.
6cc98ba
@ALGW71
Merge branch 'main' into scfv_testing
c8e60bc
@ALGW71
Add SCFV test file.
c3b2453
@ALGW71
Modify SCFv notebook.
1cef6e3
@ALGW71
Basics of MHC working - need to account for long seq length.
1ba5538
@ALGW71
Basics of MHC working - need to account for long seq length.
1ea3db6
@ALGW71
Long sequence issue sorted. Now need to explore edge cases.
7ea92d4
@ALGW71
Added cli support for mhc.
a6f9601
@ALGW71
TCR cut off implemented and continue statement skips all MHC.
9dd30be
@ALGW71
Forgot to modify score cutoff.
4d96cbc
@ALGW71
Update with new model and tweaks to classifii code.
bb80370
@ALGW71
Merge branch 'main' into MHC
d9230aa
@ALGW71
to_scheme() should not renumber MHC/HLA - these have no conversion an…
9226083 
…d will remain IMGT.
@ALGW71
The MHC chain type annotations are far from perfect - need to train m…
7b0eacf 
…ore to ensure that chain type is always correct.
@ALGW71
Found an important BUG - self.seq_type was passed to number with type…
9e94b35 
… - not classifii output.
@ALGW71 ALGW71 mentioned this pull request Sep 26, 2025
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@ALGW71