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Prototype branch#2

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AlejandroTL merged 37 commits into
mainfrom
prototype_branch
Sep 19, 2025
Merged

Prototype branch#2
AlejandroTL merged 37 commits into
mainfrom
prototype_branch

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@grpinto

@grpinto grpinto commented Jun 27, 2025

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Made the code operational :

  • made gene_resolver.py available with multiple APIs for protein, pyensembl and gene info
  • added models like borzoi and molformer
  • made gene_embeddings available with mart export and the chromosome sequences

To do :

  • Make embedder.py truly central in the code
  • add, and test text embeddings

grpinto added 15 commits April 14, 2025 09:53
@grpinto
Cleaning the file up
988750f
@grpinto
Restructured the file, added errors.py, removed blind exceptions from…
78fe53d 
… embedder.py
@grpinto
Removing the src and placing just embpy, fixing pre-commits
41a4959
@grpinto
Removing the src and placing just embpy, fixing pre-commits
6d0962c
@grpinto
Including the source again
5c1eafa
@grpinto
Added Borzoi File, created dna_models folder and added files to gitig…
9b12cef 
…nore
@grpinto
borzoi embeddings
af6ae91
@grpinto
tested borzoi
80686a9
@grpinto
Added MolFormer and ChemBerta
20e3c73
@grpinto
pseudo tested chemberta, more verifications are required
8e19dda
@grpinto
checked embed batch from enformer and borzoi and it works, fixed a bu…
790a4a7 
…g in enformer
@grpinto
Fixed gene_resolver and I can now get protein sequences and fasta seq…
2787acb 
…uences as well as gene info from MyGene.info
@grpinto
mage gene embeddings.py operational
55525aa
@grpinto
process batch works nicely
351fa97
@grpinto
added a functionality to trimm genes to this code that are bigger the…
a6bf28d 
…n the target length
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AlejandroTL
AlejandroTL reviewed Jun 27, 2025
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Comment thread src/embpy/gene_embeddings.py
AlejandroTL
AlejandroTL reviewed Jun 27, 2025
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Comment thread src/embpy/gene_embeddings.py
@AlejandroTL AlejandroTL merged commit 8153c5c into main Sep 19, 2025
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@grpinto @AlejandroTL