scripts/esm1v_ab_benchmarking.sh

#!/bin/bash

run_prediction() {
    python ../esm/examples/variant-prediction/predict.py \
        --model-location esm1v_t33_650M_UR90S_1 esm1v_t33_650M_UR90S_2 esm1v_t33_650M_UR90S_3 esm1v_t33_650M_UR90S_4 esm1v_t33_650M_UR90S_5 \
        --sequence "$1" \
        --dms-input "$2" \
        --mutation-col mutant \
        --dms-output "$3" \
        --scoring-strategy 'masked-marginals' \
        --offset-idx "$4"
}

# CR6261
run_prediction "EVQLVESGAEVKKPGSSVKVSCKASGGPFRSYAISWVRQAPGQGPEWMGGIIPIFGTTKYAPKFQGRVTITADDFAGTVYMELSSLRSEDTAMYYCAKHMGYQVRETMDVWGKGTTVTVSS" \
    "data/ab_mutagenesis_expts/cr6261/cr6261_singleMuts_exp_data.csv" \
    "output/ab_mutagenesis_expts/cr6261/cr6261_exp_data_maskMargLabeled.csv" \
    1

# CR9114
run_prediction "QVQLVQSGAEVKKPGSSVKVSCKSSGGTSNNYAISWVRQAPGQGLDWMGGISPIFGSTAYAQKFQGRVTISADIFSNTAYMELNSLTSEDTAVYFCARHGNYYYYSGMDVWGQGTTVTVSS" \
    "data/ab_mutagenesis_expts/cr9114/cr9114_singleMuts_exp_data.csv" \
    "output/ab_mutagenesis_expts/cr9114/cr9114_exp_data_maskMargLabeled.csv" \
    1

# G6 HC
run_prediction "EVQLVESGGGLVQPGGSLRLSCAASGFTISDYWIHWVRQAPGKGLEWVAGITPAGGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFVFFLPYAMDYWGQGTLVTV" \
    "data/ab_mutagenesis_expts/g6/g6_hc_exp_data.csv" \
    "output/ab_mutagenesis_expts/g6/g6Hc_exp_data_maskMargLabeled.csv" \
    1

# G6 LC
run_prediction "DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIK" \
    "data/ab_mutagenesis_expts/g6/g6_lc_exp_data.csv" \
    "output/ab_mutagenesis_expts/g6/g6Lc_exp_data_maskMargLabeled.csv" \
    1

# G6 HC (both chains)
run_prediction "EVQLVESGGGLVQPGGSLRLSCAASGFTISDYWIHWVRQAPGKGLEWVAGITPAGGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFVFFLPYAMDYWGQGTLVTVDIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIK" \
    "data/ab_mutagenesis_expts/g6/g6_hc_exp_data.csv" \
    "output/ab_mutagenesis_expts/g6/g6Hc_esm1vbothchains_exp_data_maskMargLabeled.csv" \
    1

# G6 LC (both chains)
run_prediction "EVQLVESGGGLVQPGGSLRLSCAASGFTISDYWIHWVRQAPGKGLEWVAGITPAGGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFVFFLPYAMDYWGQGTLVTVDIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIK" \
    "data/ab_mutagenesis_expts/g6/g6_lc_exp_data.csv" \
    "output/ab_mutagenesis_expts/g6/g6Lc_esm1vbothchains_exp_data_maskMargLabeled.csv" \
    -117

# CR9114 (both chains)
run_prediction "QVQLVQSGAEVKKPGSSVKVSCKSSGGTSNNYAISWVRQAPGQGLDWMGGISPIFGSTAYAQKFQGRVTISADIFSNTAYMELNSLTSEDTAVYFCARHGNYYYYSGMDVWGQGTTVTVSSQSALTQPPAVSGTPGQRVTISCSGSDSNIGRRSVNWYQQFPGTAPKLLIYSNDQRPSVVPDRFSGSKSGTSASLAISGLQSEDEAEYYCAAWDDSLKGAVFGGGTQLTVL" \
    "data/ab_mutagenesis_expts/cr9114/cr9114_singleMuts_exp_data.csv" \
    "output/ab_mutagenesis_expts/cr9114/cr9114_esm1vbothchains_exp_data_maskMargLabeled.csv" \
    1

# CR6261 (both chains)
run_prediction "EVQLVESGAEVKKPGSSVKVSCKASGGPFRSYAISWVRQAPGQGPEWMGGIIPIFGTTKYAPKFQGRVTITADDFAGTVYMELSSLRSEDTAMYYCAKHMGYQVRETMDVWGKGTTVTVSSQSVLTQPPSVSAAPGQKVTISCSGSSSNIGNDYVSWYQQLPGTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEANYYCATWDRRPTAYVVFGGGTKLTVL" \
    "data/ab_mutagenesis_expts/cr6261/cr6261_singleMuts_exp_data.csv" \
    "output/ab_mutagenesis_expts/cr6261/cr6261_esm1vbothchains_exp_data_maskMargLabeled.csv" \
    1

# CR9114 (antibody + antigen)
run_prediction "QVQLVQSGAEVKKPGSSVKVSCKSSGGTSNNYAISWVRQAPGQGLDWMGGISPIFGSTAYAQKFQGRVTISADIFSNTAYMELNSLTSEDTAVYFCARHGNYYYYSGMDVWGQGTTVTVSSQSALTQPPAVSGTPGQRVTISCSGSDSNIGRRSVNWYQQFPGTAPKLLIYSNDQRPSVVPDRFSGSKSGTSASLAISGLQSEDEAEYYCAAWDDSLKGAVFGGGTQLTVLADPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSPQRERRRKKRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSGR" \
    "data/ab_mutagenesis_expts/cr9114/cr9114_singleMuts_exp_data.csv" \
    "output/ab_mutagenesis_expts/cr9114/cr9114_esm1vAbAg_exp_data_maskMargLabeled.csv" \
    1

# CR6261 (antibody + antigen)
run_prediction "EVQLVESGAEVKKPGSSVKVSCKASGGPFRSYAISWVRQAPGQGPEWMGGIIPIFGTTKYAPKFQGRVTITADDFAGTVYMELSSLRSEDTAMYYCAKHMGYQVRETMDVWGKGTTVTVSSQSVLTQPPSVSAAPGQKVTISCSGSSSNIGNDYVSWYQQLPGTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEANYYCATWDRRPTAYVVFGGGTKLTVLADPGDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIPSIQSRGLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEIDGVSGR" \
    "data/ab_mutagenesis_expts/cr6261/cr6261_singleMuts_exp_data.csv" \
    "output/ab_mutagenesis_expts/cr6261/cr6261_esm1vAbAg_exp_data_maskMargLabeled.csv" \
    1

# G6 HC (antibody + antigen)
run_prediction "EVQLVESGGGLVQPGGSLRLSCAASGFTISDYWIHWVRQAPGKGLEWVAGITPAGGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFVFFLPYAMDYWGQGTLVTVDIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIKGQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD" \
    "data/ab_mutagenesis_expts/g6/g6_hc_exp_data.csv" \
    "output/ab_mutagenesis_expts/g6/g6Hc_esm1vAbAg_exp_data_maskMargLabeled.csv" \
    1

# G6 LC (antibody + antigen)
run_prediction "EVQLVESGGGLVQPGGSLRLSCAASGFTISDYWIHWVRQAPGKGLEWVAGITPAGGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFVFFLPYAMDYWGQGTLVTVDIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIKGQNHHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD" \
    "data/ab_mutagenesis_expts/g6/g6_lc_exp_data.csv" \
    "output/ab_mutagenesis_expts/g6/g6Lc_esm1vAbAg_exp_data_maskMargLabeled.csv" \
    -117