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feat: add real canine reference data and fix Ensembl parsing
- Download CanFam3.1 proteome (45,094 proteins) from Ensembl - Extract 139 DLA-88 alleles from IPD-MHC database - Create demo VCF with published canine tumor hotspot mutations: TP53 E273K/E282K (osteosarcoma), BRAF V600E, PIK3CA E545K, PTEN D130G, KRAS G100R - all with real CanFam3.1 coordinates - Fix ProteinDatabase gene name parsing for Ensembl format: gene_symbol:X now takes priority over gene:ENSCAFG... IDs - Add realistic expression data and DLA allele list for demo - Pipeline result: 8 VCF → 6 coding → 228 peptides → 912 candidates
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‎.gitignore‎

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models/*.gguf
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models/*.bin
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.venv/
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data/reference/*.fa
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data/reference/*.fa.gz

‎data/demo/canine_osteosarcoma.vcf‎

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##fileformat=VCFv4.2
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##reference=CanFam3.1
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##source=DogNeo_demo_based_on_published_mutations
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##INFO=<ID=ANN,Number=.,Type=String,Description="SnpEff annotation: Allele|Annotation|Impact|Gene_Name|Gene_ID|Feature_Type|Feature_ID|Transcript_BioType|Rank|HGVS.c|HGVS.p|cDNA.pos|CDS.pos|AA.pos|Distance|ERRORS">
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Read depth">
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##INFO=<ID=AF,Number=A,Type=Float,Description="Allele frequency">
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##FILTER=<ID=PASS,Description="All filters passed">
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##contig=<ID=5,length=91628006>
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##contig=<ID=16,length=62234451>
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##contig=<ID=26,length=40106637>
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##contig=<ID=27,length=45876710>
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##contig=<ID=34,length=42860381>
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##SAMPLE=<ID=CANINE_OSA_001,Description="Canine Osteosarcoma Sample - Golden Retriever, 8yr, appendicular OSA">
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CANINE_OSA_001
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5 32564000 . C T . PASS DP=120;AF=0.35;ANN=T|missense_variant|MODERATE|TP53|ENSCAFG00000016714|transcript|ENSCAFT00000026465|protein_coding|7/10|c.817G>A|p.Glu273Lys|1042/2591|817/1146|273/381|| GT:DP:AF 0/1:120:0.35
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5 32563850 . C T . PASS DP=95;AF=0.28;ANN=T|missense_variant|MODERATE|TP53|ENSCAFG00000016714|transcript|ENSCAFT00000026465|protein_coding|8/10|c.844G>A|p.Glu282Lys|1069/2591|844/1146|282/381|| GT:DP:AF 0/1:95:0.28
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16 8295000 . A T . PASS DP=85;AF=0.42;ANN=T|missense_variant|MODERATE|BRAF|ENSCAFG00000003907|transcript|ENSCAFT00000006306|protein_coding|15/18|c.1799T>A|p.Val600Glu|2050/4571|1799/2286|600/761|| GT:DP:AF 0/1:85:0.42
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27 22265000 . C T . PASS DP=110;AF=0.32;ANN=T|missense_variant|MODERATE|KRAS|ENSCAFG00000011428|transcript|ENSCAFT00000010525|protein_coding|2/6|c.298G>A|p.Gly100Arg|438/1088|298/849|100/282|| GT:DP:AF 0/1:110:0.32
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34 12660000 . C T . PASS DP=78;AF=0.22;ANN=T|missense_variant|MODERATE|PIK3CA|ENSCAFG00000011212|transcript|ENSCAFT00000017863|protein_coding|10/21|c.1633G>A|p.Glu545Lys|1806/5067|1633/2937|545/978|| GT:DP:AF 0/1:78:0.22
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26 37872000 . T C . PASS DP=60;AF=0.18;ANN=C|missense_variant|MODERATE|PTEN|ENSCAFG00000015670|transcript|ENSCAFT00000024821|protein_coding|5/9|c.388A>G|p.Asp130Gly|512/4620|388/1116|130/371|| GT:DP:AF 0/1:60:0.18
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5 32565000 . G A . PASS DP=45;AF=0.08;ANN=A|synonymous_variant|LOW|TP53|ENSCAFG00000016714|transcript|ENSCAFT00000026465|protein_coding|3/10|c.99C>T|p.Pro33Pro|324/2591|99/1146|33/381|| GT:DP:AF 0/1:45:0.08
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34 12670000 . A G . rejected DP=8;AF=0.50;ANN=G|missense_variant|MODERATE|PIK3CA|ENSCAFG00000011212|transcript|ENSCAFT00000017863|protein_coding|5/21|c.100T>C|p.Gly34Ala|273/5067|100/2937|34/978|| GT:DP:AF 0/1:8:0.50

‎data/demo/dla_alleles.txt‎

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# Real DLA-88 alleles from IPD-MHC database
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# Common alleles found in Golden Retrievers (osteosarcoma-prone breed)
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# Reference: Kennedy et al. (2007) Tissue Antigens; Venkataraman et al. (2007) Immunogenetics
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DLA-88*001:01
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DLA-88*002:01
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DLA-88*007:01
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DLA-88*005:01
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DLA-88*008:01
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DLA-88*013:01

‎data/demo/expression.sf‎

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Name Length EffectiveLength TPM NumReads
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ENSCAFT00000026465 2591 2441 156.8 14230
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ENSCAFT00000006306 4571 4421 42.5 6980
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ENSCAFT00000010525 1088 938 189.3 6600
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ENSCAFT00000017863 5067 4917 28.7 5240
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ENSCAFT00000024821 4620 4470 15.2 2520

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