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Scripts to build multiple TCRpMHC fasta based on TCRModel and IMGT database

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TCR Builder

Scripts to build multiple TCRpMHC fasta based on TCRModel and IMGT database


Input: template.csv

tcr_name,cdr3_alpha,cdr3_beta,v_and_d_alpha,j_alpha,v_and_d_beta,j_beta,peptide,imgt_hla
tcr0001,AAAAAAAAAAAAAAAAAAAAAA,BBBBBBBBBBBBBBBBBBBBBB,TRAV1-1*01,TRAJ1*01,TRBV10-1*01,TRBJ1-1*01,PPPPPPPPP,HLA00005
tcr0002,AAAAAAAAAAAAAAAAAAAAAA,BBBBBBBBBBBBBBBBBBBBBB,TRAV12-3*02,TRAJ1*01,TRBV10-1*01,TRBJ1-1*01,PPPPPPPPP,HLA00146

Usage:

mkdir output
python3 tcr_builder.py template.csv output

Output: output/tcr0001.fasta

>tcr0001_Alpha
SLEQPSEVTAVEGAIVQINCTYQTSGFYGLSWYQQHDGGAPTFLSYNALDGLEETGRFSSFLSRSDSYGYLLLQELQMKDSASYFAAAAAAAAAAAAAAAAAAAAAAGKGTRVSTSP
>tcr0001_Beta
ITQSPRHKITETGRQVTLACHQTWNHNNMFWYRQDLGHGLRLIHYSYGVQDTNKGEVSDGYSVSRSNTEDLPLTLESAASSQTSVYFBBBBBBBBBBBBBBBBBBBBBBGQGTRLTVV
>tcr0001_peptide
PPPPPPPPP
>tcr0001_HLA00005
MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPSSQPTIPIVGIIAGLVLFGAVITGAVVAAVMWRRKSSDRKGGSYSQAASSDSAQGSDVSLTACKV

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Scripts to build multiple TCRpMHC fasta based on TCRModel and IMGT database

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