notebooks/run_proteingym.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Scoring ProteinGym Data with Prime\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "from transformers import AutoTokenizer, AutoModel\n",
    "import torch\n",
    "import pandas as pd\n",
    "from Bio import SeqIO\n",
    "from tqdm.notebook import tqdm\n",
    "from pathlib import Path\n",
    "from scipy.stats import spearmanr\n",
    "\n",
    "def read_seq(seq_file):\n",
    "    for record in SeqIO.parse(seq_file, \"fasta\"):\n",
    "        return str(record.seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/limc/miniconda3/envs/plm/lib/python3.10/site-packages/huggingface_hub/file_download.py:1132: FutureWarning: `resume_download` is deprecated and will be removed in version 1.0.0. Downloads always resume when possible. If you want to force a new download, use `force_download=True`.\n",
      "  warnings.warn(\n",
      "/home/limc/miniconda3/envs/plm/lib/python3.10/site-packages/huggingface_hub/file_download.py:1132: FutureWarning: `resume_download` is deprecated and will be removed in version 1.0.0. Downloads always resume when possible. If you want to force a new download, use `force_download=True`.\n",
      "  warnings.warn(\n"
     ]
    }
   ],
   "source": [
    "model_path = \"AI4Protein/Prime_690M\"\n",
    "device = torch.device(\"cuda\" if torch.cuda.is_available() else \"cpu\")\n",
    "model = AutoModel.from_pretrained(model_path, trust_remote_code=True)\n",
    "tokenizer = AutoTokenizer.from_pretrained(model_path, trust_remote_code=True)\n",
    "model.eval()\n",
    "model = model.to(device)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "@torch.no_grad()\n",
    "def score(fasta, mutant):\n",
    "    df = pd.read_csv(mutant)\n",
    "    sequence = read_seq(fasta)\n",
    "    tokenied_results = tokenizer(sequence, return_tensors=\"pt\")\n",
    "    input_ids = tokenied_results.input_ids.to(device)\n",
    "    attention_mask = tokenied_results.attention_mask.to(device)\n",
    "    logits = model(input_ids, attention_mask=attention_mask).logits[0, 1:-1, :].log_softmax(dim=-1)\n",
    "    scores = []\n",
    "    for mutant in df[\"mutant\"]:\n",
    "        score = 0\n",
    "        for sub_mutant in mutant.split(\":\"):\n",
    "            wt, idx, mt = sub_mutant[0], int(sub_mutant[1:-1]) - 1, sub_mutant[-1]\n",
    "            score += (logits[idx, tokenizer.get_vocab()[mt]] - logits[idx, tokenizer.get_vocab()[wt]]).item()\n",
    "        scores.append(score)\n",
    "    df[\"predict_score\"] = scores\n",
    "    return df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "sequence_folder = Path(\"../proteingym_v1.0_fasta/fasta\")\n",
    "mutant_folder = Path(\"../proteingym_v1.0_fasta/mutant\")\n",
    "output_folder = Path(\"../proteingym_v1.0_fasta/scores\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Scoring RL40A_YEAST_Roscoe_2013, rs = 0.6550, saved to ../proteingym_v1.0_fasta/scores/RL40A_YEAST_Roscoe_2013.csv\n",
      "Scoring RL40A_YEAST_Mavor_2016, rs = 0.5691, saved to ../proteingym_v1.0_fasta/scores/RL40A_YEAST_Mavor_2016.csv\n",
      "Scoring RCRO_LAMBD_Tsuboyama_2023_1ORC, rs = 0.6436, saved to ../proteingym_v1.0_fasta/scores/RCRO_LAMBD_Tsuboyama_2023_1ORC.csv\n",
      "Scoring RD23A_HUMAN_Tsuboyama_2023_1IFY, rs = 0.5803, saved to ../proteingym_v1.0_fasta/scores/RD23A_HUMAN_Tsuboyama_2023_1IFY.csv\n",
      "Scoring RDRP_I33A0_Li_2023, rs = 0.3237, saved to ../proteingym_v1.0_fasta/scores/RDRP_I33A0_Li_2023.csv\n",
      "Scoring REV_HV1H2_Fernandes_2016, rs = 0.3174, saved to ../proteingym_v1.0_fasta/scores/REV_HV1H2_Fernandes_2016.csv\n",
      "Scoring RFAH_ECOLI_Tsuboyama_2023_2LCL, rs = 0.3725, saved to ../proteingym_v1.0_fasta/scores/RFAH_ECOLI_Tsuboyama_2023_2LCL.csv\n",
      "Scoring RL20_AQUAE_Tsuboyama_2023_1GYZ, rs = 0.7586, saved to ../proteingym_v1.0_fasta/scores/RL20_AQUAE_Tsuboyama_2023_1GYZ.csv\n",
      "Scoring RASH_HUMAN_Bandaru_2017, rs = 0.5398, saved to ../proteingym_v1.0_fasta/scores/RASH_HUMAN_Bandaru_2017.csv\n",
      "Scoring RASK_HUMAN_Weng_2022_abundance, rs = 0.2740, saved to ../proteingym_v1.0_fasta/scores/RASK_HUMAN_Weng_2022_abundance.csv\n",
      "Scoring RASK_HUMAN_Weng_2022_binding-DARPin_K55, rs = 0.6174, saved to ../proteingym_v1.0_fasta/scores/RASK_HUMAN_Weng_2022_binding-DARPin_K55.csv\n",
      "Scoring RBP1_HUMAN_Tsuboyama_2023_2KWH, rs = 0.5806, saved to ../proteingym_v1.0_fasta/scores/RBP1_HUMAN_Tsuboyama_2023_2KWH.csv\n",
      "Scoring RCD1_ARATH_Tsuboyama_2023_5OAO, rs = 0.5760, saved to ../proteingym_v1.0_fasta/scores/RCD1_ARATH_Tsuboyama_2023_5OAO.csv\n",
      "Scoring Q8WTC7_9CNID_Somermeyer_2022, rs = 0.2718, saved to ../proteingym_v1.0_fasta/scores/Q8WTC7_9CNID_Somermeyer_2022.csv\n",
      "Scoring R1AB_SARS2_Flynn_2022, rs = 0.2749, saved to ../proteingym_v1.0_fasta/scores/R1AB_SARS2_Flynn_2022.csv\n",
      "Scoring RAD_ANTMA_Tsuboyama_2023_2CJJ, rs = 0.5129, saved to ../proteingym_v1.0_fasta/scores/RAD_ANTMA_Tsuboyama_2023_2CJJ.csv\n",
      "Scoring RAF1_HUMAN_Zinkus-Boltz_2019, rs = 0.4598, saved to ../proteingym_v1.0_fasta/scores/RAF1_HUMAN_Zinkus-Boltz_2019.csv\n",
      "Scoring PRKN_HUMAN_Clausen_2023, rs = 0.5534, saved to ../proteingym_v1.0_fasta/scores/PRKN_HUMAN_Clausen_2023.csv\n",
      "Scoring PSAE_SYNP2_Tsuboyama_2023_1PSE, rs = 0.7370, saved to ../proteingym_v1.0_fasta/scores/PSAE_SYNP2_Tsuboyama_2023_1PSE.csv\n",
      "Scoring PTEN_HUMAN_Matreyek_2021, rs = 0.4983, saved to ../proteingym_v1.0_fasta/scores/PTEN_HUMAN_Matreyek_2021.csv\n",
      "Scoring PTEN_HUMAN_Mighell_2018, rs = 0.5441, saved to ../proteingym_v1.0_fasta/scores/PTEN_HUMAN_Mighell_2018.csv\n",
      "Scoring Q2N0S5_9HIV1_Haddox_2018, rs = 0.3432, saved to ../proteingym_v1.0_fasta/scores/Q2N0S5_9HIV1_Haddox_2018.csv\n",
      "Scoring Q53Z42_HUMAN_McShan_2019_binding-TAPBPR, rs = 0.3095, saved to ../proteingym_v1.0_fasta/scores/Q53Z42_HUMAN_McShan_2019_binding-TAPBPR.csv\n",
      "Scoring Q53Z42_HUMAN_McShan_2019_expression, rs = 0.5889, saved to ../proteingym_v1.0_fasta/scores/Q53Z42_HUMAN_McShan_2019_expression.csv\n",
      "Scoring Q59976_STRSQ_Romero_2015, rs = 0.6691, saved to ../proteingym_v1.0_fasta/scores/Q59976_STRSQ_Romero_2015.csv\n",
      "Scoring Q6WV13_9MAXI_Somermeyer_2022, rs = 0.3104, saved to ../proteingym_v1.0_fasta/scores/Q6WV13_9MAXI_Somermeyer_2022.csv\n",
      "Scoring Q837P4_ENTFA_Meier_2023, rs = 0.6395, saved to ../proteingym_v1.0_fasta/scores/Q837P4_ENTFA_Meier_2023.csv\n",
      "Scoring Q837P5_ENTFA_Meier_2023, rs = 0.5921, saved to ../proteingym_v1.0_fasta/scores/Q837P5_ENTFA_Meier_2023.csv\n",
      "Scoring PA_I34A1_Wu_2015, rs = 0.1978, saved to ../proteingym_v1.0_fasta/scores/PA_I34A1_Wu_2015.csv\n",
      "Scoring PHOT_CHLRE_Chen_2023, rs = 0.5800, saved to ../proteingym_v1.0_fasta/scores/PHOT_CHLRE_Chen_2023.csv\n",
      "Scoring PIN1_HUMAN_Tsuboyama_2023_1I6C, rs = 0.7271, saved to ../proteingym_v1.0_fasta/scores/PIN1_HUMAN_Tsuboyama_2023_1I6C.csv\n",
      "Scoring PITX2_HUMAN_Tsuboyama_2023_2L7M, rs = 0.6600, saved to ../proteingym_v1.0_fasta/scores/PITX2_HUMAN_Tsuboyama_2023_2L7M.csv\n",
      "Scoring PKN1_HUMAN_Tsuboyama_2023_1URF, rs = 0.3843, saved to ../proteingym_v1.0_fasta/scores/PKN1_HUMAN_Tsuboyama_2023_1URF.csv\n",
      "Scoring POLG_CXB3N_Mattenberger_2021, rs = 0.3765, saved to ../proteingym_v1.0_fasta/scores/POLG_CXB3N_Mattenberger_2021.csv\n",
      "Scoring POLG_DEN26_Suphatrakul_2023, rs = 0.2977, saved to ../proteingym_v1.0_fasta/scores/POLG_DEN26_Suphatrakul_2023.csv\n",
      "Scoring POLG_HCVJF_Qi_2014, rs = 0.4021, saved to ../proteingym_v1.0_fasta/scores/POLG_HCVJF_Qi_2014.csv\n",
      "Scoring POLG_PESV_Tsuboyama_2023_2MXD, rs = 0.6410, saved to ../proteingym_v1.0_fasta/scores/POLG_PESV_Tsuboyama_2023_2MXD.csv\n",
      "Scoring PPARG_HUMAN_Majithia_2016, rs = 0.5683, saved to ../proteingym_v1.0_fasta/scores/PPARG_HUMAN_Majithia_2016.csv\n",
      "Scoring PPM1D_HUMAN_Miller_2022, rs = 0.6049, saved to ../proteingym_v1.0_fasta/scores/PPM1D_HUMAN_Miller_2022.csv\n",
      "Scoring PR40A_HUMAN_Tsuboyama_2023_1UZC, rs = 0.8333, saved to ../proteingym_v1.0_fasta/scores/PR40A_HUMAN_Tsuboyama_2023_1UZC.csv\n",
      "Scoring LYAM1_HUMAN_Elazar_2016, rs = 0.4657, saved to ../proteingym_v1.0_fasta/scores/LYAM1_HUMAN_Elazar_2016.csv\n",
      "Scoring MAFG_MOUSE_Tsuboyama_2023_1K1V, rs = 0.6552, saved to ../proteingym_v1.0_fasta/scores/MAFG_MOUSE_Tsuboyama_2023_1K1V.csv\n",
      "Scoring MBD11_ARATH_Tsuboyama_2023_6ACV, rs = 0.8223, saved to ../proteingym_v1.0_fasta/scores/MBD11_ARATH_Tsuboyama_2023_6ACV.csv\n",
      "Scoring MET_HUMAN_Estevam_2023, rs = 0.6061, saved to ../proteingym_v1.0_fasta/scores/MET_HUMAN_Estevam_2023.csv\n",
      "Scoring MK01_HUMAN_Brenan_2016, rs = 0.2008, saved to ../proteingym_v1.0_fasta/scores/MK01_HUMAN_Brenan_2016.csv\n",
      "Scoring MLAC_ECOLI_MacRae_2023, rs = 0.4749, saved to ../proteingym_v1.0_fasta/scores/MLAC_ECOLI_MacRae_2023.csv\n",
      "Scoring MSH2_HUMAN_Jia_2020, rs = 0.3947, saved to ../proteingym_v1.0_fasta/scores/MSH2_HUMAN_Jia_2020.csv\n",
      "Scoring MTH3_HAEAE_RockahShmuel_2015, rs = 0.6271, saved to ../proteingym_v1.0_fasta/scores/MTH3_HAEAE_RockahShmuel_2015.csv\n",
      "Scoring MTHR_HUMAN_Weile_2021, rs = 0.3812, saved to ../proteingym_v1.0_fasta/scores/MTHR_HUMAN_Weile_2021.csv\n",
      "Scoring MYO3_YEAST_Tsuboyama_2023_2BTT, rs = 0.6353, saved to ../proteingym_v1.0_fasta/scores/MYO3_YEAST_Tsuboyama_2023_2BTT.csv\n",
      "Scoring NCAP_I34A1_Doud_2015, rs = 0.1626, saved to ../proteingym_v1.0_fasta/scores/NCAP_I34A1_Doud_2015.csv\n",
      "Scoring NKX31_HUMAN_Tsuboyama_2023_2L9R, rs = 0.7105, saved to ../proteingym_v1.0_fasta/scores/NKX31_HUMAN_Tsuboyama_2023_2L9R.csv\n",
      "Scoring NPC1_HUMAN_Erwood_2022_HEK293T, rs = 0.7219, saved to ../proteingym_v1.0_fasta/scores/NPC1_HUMAN_Erwood_2022_HEK293T.csv\n",
      "Scoring NPC1_HUMAN_Erwood_2022_RPE1, rs = 0.7096, saved to ../proteingym_v1.0_fasta/scores/NPC1_HUMAN_Erwood_2022_RPE1.csv\n",
      "Scoring NRAM_I33A0_Jiang_2016, rs = 0.2787, saved to ../proteingym_v1.0_fasta/scores/NRAM_I33A0_Jiang_2016.csv\n",
      "Scoring NUD15_HUMAN_Suiter_2020, rs = 0.5956, saved to ../proteingym_v1.0_fasta/scores/NUD15_HUMAN_Suiter_2020.csv\n",
      "Scoring NUSA_ECOLI_Tsuboyama_2023_1WCL, rs = 0.6518, saved to ../proteingym_v1.0_fasta/scores/NUSA_ECOLI_Tsuboyama_2023_1WCL.csv\n",
      "Scoring NUSG_MYCTU_Tsuboyama_2023_2MI6, rs = 0.6157, saved to ../proteingym_v1.0_fasta/scores/NUSG_MYCTU_Tsuboyama_2023_2MI6.csv\n",
      "Scoring OBSCN_HUMAN_Tsuboyama_2023_1V1C, rs = 0.8204, saved to ../proteingym_v1.0_fasta/scores/OBSCN_HUMAN_Tsuboyama_2023_1V1C.csv\n",
      "Scoring ODP2_GEOSE_Tsuboyama_2023_1W4G, rs = 0.1516, saved to ../proteingym_v1.0_fasta/scores/ODP2_GEOSE_Tsuboyama_2023_1W4G.csv\n",
      "Scoring OPSD_HUMAN_Wan_2019, rs = 0.6343, saved to ../proteingym_v1.0_fasta/scores/OPSD_HUMAN_Wan_2019.csv\n",
      "Scoring OTC_HUMAN_Lo_2023, rs = 0.5917, saved to ../proteingym_v1.0_fasta/scores/OTC_HUMAN_Lo_2023.csv\n",
      "Scoring OTU7A_HUMAN_Tsuboyama_2023_2L2D, rs = 0.5484, saved to ../proteingym_v1.0_fasta/scores/OTU7A_HUMAN_Tsuboyama_2023_2L2D.csv\n",
      "Scoring OXDA_RHOTO_Vanella_2023_activity, rs = 0.4067, saved to ../proteingym_v1.0_fasta/scores/OXDA_RHOTO_Vanella_2023_activity.csv\n",
      "Scoring OXDA_RHOTO_Vanella_2023_expression, rs = 0.3333, saved to ../proteingym_v1.0_fasta/scores/OXDA_RHOTO_Vanella_2023_expression.csv\n",
      "Scoring P53_HUMAN_Giacomelli_2018_Null_Etoposide, rs = 0.4924, saved to ../proteingym_v1.0_fasta/scores/P53_HUMAN_Giacomelli_2018_Null_Etoposide.csv\n",
      "Scoring P53_HUMAN_Giacomelli_2018_Null_Nutlin, rs = 0.4611, saved to ../proteingym_v1.0_fasta/scores/P53_HUMAN_Giacomelli_2018_Null_Nutlin.csv\n",
      "Scoring P53_HUMAN_Giacomelli_2018_WT_Nutlin, rs = 0.4527, saved to ../proteingym_v1.0_fasta/scores/P53_HUMAN_Giacomelli_2018_WT_Nutlin.csv\n",
      "Scoring P53_HUMAN_Kotler_2018, rs = 0.7041, saved to ../proteingym_v1.0_fasta/scores/P53_HUMAN_Kotler_2018.csv\n",
      "Scoring P84126_THETH_Chan_2017, rs = 0.6656, saved to ../proteingym_v1.0_fasta/scores/P84126_THETH_Chan_2017.csv\n",
      "Scoring PABP_YEAST_Melamed_2013, rs = 0.7718, saved to ../proteingym_v1.0_fasta/scores/PABP_YEAST_Melamed_2013.csv\n",
      "Scoring PAI1_HUMAN_Huttinger_2021, rs = 0.4690, saved to ../proteingym_v1.0_fasta/scores/PAI1_HUMAN_Huttinger_2021.csv\n",
      "Scoring I6TAH8_I68A0_Doud_2015, rs = 0.1261, saved to ../proteingym_v1.0_fasta/scores/I6TAH8_I68A0_Doud_2015.csv\n",
      "Scoring IF1_ECOLI_Kelsic_2016, rs = 0.5836, saved to ../proteingym_v1.0_fasta/scores/IF1_ECOLI_Kelsic_2016.csv\n",
      "Scoring ILF3_HUMAN_Tsuboyama_2023_2L33, rs = 0.4886, saved to ../proteingym_v1.0_fasta/scores/ILF3_HUMAN_Tsuboyama_2023_2L33.csv\n",
      "Scoring ISDH_STAAW_Tsuboyama_2023_2LHR, rs = 0.5226, saved to ../proteingym_v1.0_fasta/scores/ISDH_STAAW_Tsuboyama_2023_2LHR.csv\n",
      "Scoring KCNE1_HUMAN_Muhammad_2023_expression, rs = 0.0596, saved to ../proteingym_v1.0_fasta/scores/KCNE1_HUMAN_Muhammad_2023_expression.csv\n",
      "Scoring KCNE1_HUMAN_Muhammad_2023_function, rs = 0.5705, saved to ../proteingym_v1.0_fasta/scores/KCNE1_HUMAN_Muhammad_2023_function.csv\n",
      "Scoring KCNH2_HUMAN_Kozek_2020, rs = 0.5792, saved to ../proteingym_v1.0_fasta/scores/KCNH2_HUMAN_Kozek_2020.csv\n",
      "Scoring KCNJ2_MOUSE_Coyote-Maestas_2022_function, rs = 0.3799, saved to ../proteingym_v1.0_fasta/scores/KCNJ2_MOUSE_Coyote-Maestas_2022_function.csv\n",
      "Scoring KCNJ2_MOUSE_Coyote-Maestas_2022_surface, rs = 0.3488, saved to ../proteingym_v1.0_fasta/scores/KCNJ2_MOUSE_Coyote-Maestas_2022_surface.csv\n",
      "Scoring KKA2_KLEPN_Melnikov_2014, rs = 0.6617, saved to ../proteingym_v1.0_fasta/scores/KKA2_KLEPN_Melnikov_2014.csv\n",
      "Scoring LGK_LIPST_Klesmith_2015, rs = 0.5764, saved to ../proteingym_v1.0_fasta/scores/LGK_LIPST_Klesmith_2015.csv\n",
      "Scoring HXK4_HUMAN_Gersing_2022_activity, rs = 0.5226, saved to ../proteingym_v1.0_fasta/scores/HXK4_HUMAN_Gersing_2022_activity.csv\n",
      "Scoring HXK4_HUMAN_Gersing_2023_abundance, rs = 0.3970, saved to ../proteingym_v1.0_fasta/scores/HXK4_HUMAN_Gersing_2023_abundance.csv\n",
      "Scoring HSP82_YEAST_Flynn_2019, rs = 0.4075, saved to ../proteingym_v1.0_fasta/scores/HSP82_YEAST_Flynn_2019.csv\n",
      "Scoring HSP82_YEAST_Mishra_2016, rs = 0.5586, saved to ../proteingym_v1.0_fasta/scores/HSP82_YEAST_Mishra_2016.csv\n",
      "Scoring HEM3_HUMAN_Loggerenberg_2023, rs = 0.4204, saved to ../proteingym_v1.0_fasta/scores/HEM3_HUMAN_Loggerenberg_2023.csv\n",
      "Scoring HIS7_YEAST_Pokusaeva_2019, rs = 0.5112, saved to ../proteingym_v1.0_fasta/scores/HIS7_YEAST_Pokusaeva_2019.csv\n",
      "Scoring HMDH_HUMAN_Jiang_2019, rs = 0.4721, saved to ../proteingym_v1.0_fasta/scores/HMDH_HUMAN_Jiang_2019.csv\n",
      "Scoring HSP82_YEAST_Cote-Hammarlof_2020_growth-H2O2, rs = 0.3471, saved to ../proteingym_v1.0_fasta/scores/HSP82_YEAST_Cote-Hammarlof_2020_growth-H2O2.csv\n",
      "Scoring CP2C9_HUMAN_Amorosi_2021_abundance, rs = 0.6657, saved to ../proteingym_v1.0_fasta/scores/CP2C9_HUMAN_Amorosi_2021_abundance.csv\n",
      "Scoring CP2C9_HUMAN_Amorosi_2021_activity, rs = 0.6912, saved to ../proteingym_v1.0_fasta/scores/CP2C9_HUMAN_Amorosi_2021_activity.csv\n",
      "Scoring CSN4_MOUSE_Tsuboyama_2023_1UFM, rs = 0.5416, saved to ../proteingym_v1.0_fasta/scores/CSN4_MOUSE_Tsuboyama_2023_1UFM.csv\n",
      "Scoring CUE1_YEAST_Tsuboyama_2023_2MYX, rs = 0.5907, saved to ../proteingym_v1.0_fasta/scores/CUE1_YEAST_Tsuboyama_2023_2MYX.csv\n",
      "Scoring D7PM05_CLYGR_Somermeyer_2022, rs = 0.5309, saved to ../proteingym_v1.0_fasta/scores/D7PM05_CLYGR_Somermeyer_2022.csv\n",
      "Scoring DLG4_HUMAN_Faure_2021, rs = 0.6529, saved to ../proteingym_v1.0_fasta/scores/DLG4_HUMAN_Faure_2021.csv\n",
      "Scoring DLG4_RAT_McLaughlin_2012, rs = 0.5463, saved to ../proteingym_v1.0_fasta/scores/DLG4_RAT_McLaughlin_2012.csv\n",
      "Scoring DN7A_SACS2_Tsuboyama_2023_1JIC, rs = 0.5297, saved to ../proteingym_v1.0_fasta/scores/DN7A_SACS2_Tsuboyama_2023_1JIC.csv\n",
      "Scoring DNJA1_HUMAN_Tsuboyama_2023_2LO1, rs = 0.8488, saved to ../proteingym_v1.0_fasta/scores/DNJA1_HUMAN_Tsuboyama_2023_2LO1.csv\n",
      "Scoring DOCK1_MOUSE_Tsuboyama_2023_2M0Y, rs = 0.6189, saved to ../proteingym_v1.0_fasta/scores/DOCK1_MOUSE_Tsuboyama_2023_2M0Y.csv\n",
      "Scoring DYR_ECOLI_Nguyen_2023, rs = 0.5234, saved to ../proteingym_v1.0_fasta/scores/DYR_ECOLI_Nguyen_2023.csv\n",
      "Scoring DYR_ECOLI_Thompson_2019, rs = 0.5145, saved to ../proteingym_v1.0_fasta/scores/DYR_ECOLI_Thompson_2019.csv\n",
      "Scoring ENVZ_ECOLI_Ghose_2023, rs = 0.2177, saved to ../proteingym_v1.0_fasta/scores/ENVZ_ECOLI_Ghose_2023.csv\n",
      "Scoring ENV_HV1B9_DuenasDecamp_2016, rs = 0.2940, saved to ../proteingym_v1.0_fasta/scores/ENV_HV1B9_DuenasDecamp_2016.csv\n",
      "Scoring ENV_HV1BR_Haddox_2016, rs = 0.2020, saved to ../proteingym_v1.0_fasta/scores/ENV_HV1BR_Haddox_2016.csv\n",
      "Scoring EPHB2_HUMAN_Tsuboyama_2023_1F0M, rs = 0.8521, saved to ../proteingym_v1.0_fasta/scores/EPHB2_HUMAN_Tsuboyama_2023_1F0M.csv\n",
      "Scoring ERBB2_HUMAN_Elazar_2016, rs = 0.5367, saved to ../proteingym_v1.0_fasta/scores/ERBB2_HUMAN_Elazar_2016.csv\n",
      "Scoring ESTA_BACSU_Nutschel_2020, rs = 0.3109, saved to ../proteingym_v1.0_fasta/scores/ESTA_BACSU_Nutschel_2020.csv\n",
      "Scoring F7YBW7_MESOW_Ding_2023, rs = 0.5520, saved to ../proteingym_v1.0_fasta/scores/F7YBW7_MESOW_Ding_2023.csv\n",
      "Scoring F7YBW8_MESOW_Aakre_2015, rs = 0.4592, saved to ../proteingym_v1.0_fasta/scores/F7YBW8_MESOW_Aakre_2015.csv\n",
      "Scoring FECA_ECOLI_Tsuboyama_2023_2D1U, rs = 0.5717, saved to ../proteingym_v1.0_fasta/scores/FECA_ECOLI_Tsuboyama_2023_2D1U.csv\n",
      "Scoring FKBP3_HUMAN_Tsuboyama_2023_2KFV, rs = 0.4191, saved to ../proteingym_v1.0_fasta/scores/FKBP3_HUMAN_Tsuboyama_2023_2KFV.csv\n",
      "Scoring GAL4_YEAST_Kitzman_2015, rs = 0.6740, saved to ../proteingym_v1.0_fasta/scores/GAL4_YEAST_Kitzman_2015.csv\n",
      "Scoring GCN4_YEAST_Staller_2018, rs = 0.2366, saved to ../proteingym_v1.0_fasta/scores/GCN4_YEAST_Staller_2018.csv\n",
      "Scoring GDIA_HUMAN_Silverstein_2021, rs = 0.4452, saved to ../proteingym_v1.0_fasta/scores/GDIA_HUMAN_Silverstein_2021.csv\n",
      "Scoring GFP_AEQVI_Sarkisyan_2016, rs = 0.6098, saved to ../proteingym_v1.0_fasta/scores/GFP_AEQVI_Sarkisyan_2016.csv\n",
      "Scoring GLPA_HUMAN_Elazar_2016, rs = 0.4692, saved to ../proteingym_v1.0_fasta/scores/GLPA_HUMAN_Elazar_2016.csv\n",
      "Scoring GRB2_HUMAN_Faure_2021, rs = 0.6744, saved to ../proteingym_v1.0_fasta/scores/GRB2_HUMAN_Faure_2021.csv\n",
      "Scoring HCP_LAMBD_Tsuboyama_2023_2L6Q, rs = 0.7102, saved to ../proteingym_v1.0_fasta/scores/HCP_LAMBD_Tsuboyama_2023_2L6Q.csv\n",
      "Scoring HECD1_HUMAN_Tsuboyama_2023_3DKM, rs = 0.3892, saved to ../proteingym_v1.0_fasta/scores/HECD1_HUMAN_Tsuboyama_2023_3DKM.csv\n",
      "Scoring CALM1_HUMAN_Weile_2017, rs = 0.1954, saved to ../proteingym_v1.0_fasta/scores/CALM1_HUMAN_Weile_2017.csv\n",
      "Scoring CAPSD_AAV2S_Sinai_2021, rs = 0.2355, saved to ../proteingym_v1.0_fasta/scores/CAPSD_AAV2S_Sinai_2021.csv\n",
      "Scoring CAR11_HUMAN_Meitlis_2020_gof, rs = 0.3333, saved to ../proteingym_v1.0_fasta/scores/CAR11_HUMAN_Meitlis_2020_gof.csv\n",
      "Scoring CAR11_HUMAN_Meitlis_2020_lof, rs = 0.5002, saved to ../proteingym_v1.0_fasta/scores/CAR11_HUMAN_Meitlis_2020_lof.csv\n",
      "Scoring CAS9_STRP1_Spencer_2017_positive, rs = 0.1924, saved to ../proteingym_v1.0_fasta/scores/CAS9_STRP1_Spencer_2017_positive.csv\n",
      "Scoring CASP3_HUMAN_Roychowdhury_2020, rs = 0.6361, saved to ../proteingym_v1.0_fasta/scores/CASP3_HUMAN_Roychowdhury_2020.csv\n",
      "Scoring CASP7_HUMAN_Roychowdhury_2020, rs = 0.6361, saved to ../proteingym_v1.0_fasta/scores/CASP7_HUMAN_Roychowdhury_2020.csv\n",
      "Scoring CATR_CHLRE_Tsuboyama_2023_2AMI, rs = 0.7260, saved to ../proteingym_v1.0_fasta/scores/CATR_CHLRE_Tsuboyama_2023_2AMI.csv\n",
      "Scoring CBPA2_HUMAN_Tsuboyama_2023_1O6X, rs = 0.7866, saved to ../proteingym_v1.0_fasta/scores/CBPA2_HUMAN_Tsuboyama_2023_1O6X.csv\n",
      "Scoring CBS_HUMAN_Sun_2020, rs = 0.3432, saved to ../proteingym_v1.0_fasta/scores/CBS_HUMAN_Sun_2020.csv\n",
      "Scoring CBX4_HUMAN_Tsuboyama_2023_2K28, rs = 0.7380, saved to ../proteingym_v1.0_fasta/scores/CBX4_HUMAN_Tsuboyama_2023_2K28.csv\n",
      "Scoring CCDB_ECOLI_Adkar_2012, rs = 0.5307, saved to ../proteingym_v1.0_fasta/scores/CCDB_ECOLI_Adkar_2012.csv\n",
      "Scoring CCDB_ECOLI_Tripathi_2016, rs = 0.5450, saved to ../proteingym_v1.0_fasta/scores/CCDB_ECOLI_Tripathi_2016.csv\n",
      "Scoring CCR5_HUMAN_Gill_2023, rs = 0.3372, saved to ../proteingym_v1.0_fasta/scores/CCR5_HUMAN_Gill_2023.csv\n",
      "Scoring CD19_HUMAN_Klesmith_2019_FMC_singles, rs = 0.0774, saved to ../proteingym_v1.0_fasta/scores/CD19_HUMAN_Klesmith_2019_FMC_singles.csv\n",
      "Scoring A4D664_9INFA_Soh_2019, rs = 0.2322, saved to ../proteingym_v1.0_fasta/scores/A4D664_9INFA_Soh_2019.csv\n",
      "Scoring A4GRB6_PSEAI_Chen_2020, rs = 0.7594, saved to ../proteingym_v1.0_fasta/scores/A4GRB6_PSEAI_Chen_2020.csv\n",
      "Scoring A4_HUMAN_Seuma_2022, rs = 0.4939, saved to ../proteingym_v1.0_fasta/scores/A4_HUMAN_Seuma_2022.csv\n",
      "Scoring AACC1_PSEAI_Dandage_2018, rs = 0.4664, saved to ../proteingym_v1.0_fasta/scores/AACC1_PSEAI_Dandage_2018.csv\n",
      "Scoring ACE2_HUMAN_Chan_2020, rs = 0.2483, saved to ../proteingym_v1.0_fasta/scores/ACE2_HUMAN_Chan_2020.csv\n",
      "Scoring ADRB2_HUMAN_Jones_2020, rs = 0.5223, saved to ../proteingym_v1.0_fasta/scores/ADRB2_HUMAN_Jones_2020.csv\n",
      "Scoring AICDA_HUMAN_Gajula_2014_3cycles, rs = 0.4037, saved to ../proteingym_v1.0_fasta/scores/AICDA_HUMAN_Gajula_2014_3cycles.csv\n",
      "Scoring AMFR_HUMAN_Tsuboyama_2023_4G3O, rs = 0.3081, saved to ../proteingym_v1.0_fasta/scores/AMFR_HUMAN_Tsuboyama_2023_4G3O.csv\n",
      "Scoring AMIE_PSEAE_Wrenbeck_2017, rs = 0.6411, saved to ../proteingym_v1.0_fasta/scores/AMIE_PSEAE_Wrenbeck_2017.csv\n",
      "Scoring ANCSZ_Hobbs_2022, rs = 0.6000, saved to ../proteingym_v1.0_fasta/scores/ANCSZ_Hobbs_2022.csv\n",
      "Scoring ARGR_ECOLI_Tsuboyama_2023_1AOY, rs = 0.6190, saved to ../proteingym_v1.0_fasta/scores/ARGR_ECOLI_Tsuboyama_2023_1AOY.csv\n",
      "Scoring B2L11_HUMAN_Dutta_2010_binding-Mcl-1, rs = 0.5131, saved to ../proteingym_v1.0_fasta/scores/B2L11_HUMAN_Dutta_2010_binding-Mcl-1.csv\n",
      "Scoring BBC1_YEAST_Tsuboyama_2023_1TG0, rs = 0.5040, saved to ../proteingym_v1.0_fasta/scores/BBC1_YEAST_Tsuboyama_2023_1TG0.csv\n",
      "Scoring BCHB_CHLTE_Tsuboyama_2023_2KRU, rs = 0.5998, saved to ../proteingym_v1.0_fasta/scores/BCHB_CHLTE_Tsuboyama_2023_2KRU.csv\n",
      "Scoring BLAT_ECOLX_Deng_2012, rs = 0.5468, saved to ../proteingym_v1.0_fasta/scores/BLAT_ECOLX_Deng_2012.csv\n",
      "Scoring BLAT_ECOLX_Firnberg_2014, rs = 0.8029, saved to ../proteingym_v1.0_fasta/scores/BLAT_ECOLX_Firnberg_2014.csv\n",
      "Scoring BLAT_ECOLX_Jacquier_2013, rs = 0.7530, saved to ../proteingym_v1.0_fasta/scores/BLAT_ECOLX_Jacquier_2013.csv\n",
      "Scoring BLAT_ECOLX_Stiffler_2015, rs = 0.7964, saved to ../proteingym_v1.0_fasta/scores/BLAT_ECOLX_Stiffler_2015.csv\n",
      "Scoring BRCA1_HUMAN_Findlay_2018, rs = 0.5291, saved to ../proteingym_v1.0_fasta/scores/BRCA1_HUMAN_Findlay_2018.csv\n",
      "Scoring BRCA2_HUMAN_Erwood_2022_HEK293T, rs = 0.4141, saved to ../proteingym_v1.0_fasta/scores/BRCA2_HUMAN_Erwood_2022_HEK293T.csv\n",
      "Scoring C6KNH7_9INFA_Lee_2018, rs = 0.4974, saved to ../proteingym_v1.0_fasta/scores/C6KNH7_9INFA_Lee_2018.csv\n",
      "Scoring A0A2Z5U3Z0_9INFA_Wu_2014, rs = 0.4836, saved to ../proteingym_v1.0_fasta/scores/A0A2Z5U3Z0_9INFA_Wu_2014.csv\n",
      "Scoring A0A192B1T2_9HIV1_Haddox_2018, rs = 0.3399, saved to ../proteingym_v1.0_fasta/scores/A0A192B1T2_9HIV1_Haddox_2018.csv\n",
      "Scoring A0A1I9GEU1_NEIME_Kennouche_2019, rs = 0.1121, saved to ../proteingym_v1.0_fasta/scores/A0A1I9GEU1_NEIME_Kennouche_2019.csv\n",
      "Scoring A0A247D711_LISMN_Stadelmann_2021, rs = 0.3404, saved to ../proteingym_v1.0_fasta/scores/A0A247D711_LISMN_Stadelmann_2021.csv\n",
      "Scoring A0A2Z5U3Z0_9INFA_Doud_2016, rs = 0.5831, saved to ../proteingym_v1.0_fasta/scores/A0A2Z5U3Z0_9INFA_Doud_2016.csv\n",
      "Scoring A0A140D2T1_ZIKV_Sourisseau_2019, rs = 0.2028, saved to ../proteingym_v1.0_fasta/scores/A0A140D2T1_ZIKV_Sourisseau_2019.csv\n",
      "Scoring RL40A_YEAST_Roscoe_2014, rs = 0.6343, saved to ../proteingym_v1.0_fasta/scores/RL40A_YEAST_Roscoe_2014.csv\n",
      "Scoring RNC_ECOLI_Weeks_2023, rs = 0.5975, saved to ../proteingym_v1.0_fasta/scores/RNC_ECOLI_Weeks_2023.csv\n",
      "Scoring RPC1_BP434_Tsuboyama_2023_1R69, rs = 0.7619, saved to ../proteingym_v1.0_fasta/scores/RPC1_BP434_Tsuboyama_2023_1R69.csv\n",
      "Scoring RPC1_LAMBD_Li_2019_high-expression, rs = 0.5887, saved to ../proteingym_v1.0_fasta/scores/RPC1_LAMBD_Li_2019_high-expression.csv\n",
      "Scoring RPC1_LAMBD_Li_2019_low-expression, rs = 0.6255, saved to ../proteingym_v1.0_fasta/scores/RPC1_LAMBD_Li_2019_low-expression.csv\n",
      "Scoring RS15_GEOSE_Tsuboyama_2023_1A32, rs = 0.4681, saved to ../proteingym_v1.0_fasta/scores/RS15_GEOSE_Tsuboyama_2023_1A32.csv\n",
      "Scoring S22A1_HUMAN_Yee_2023_abundance, rs = 0.6419, saved to ../proteingym_v1.0_fasta/scores/S22A1_HUMAN_Yee_2023_abundance.csv\n",
      "Scoring S22A1_HUMAN_Yee_2023_activity, rs = 0.6074, saved to ../proteingym_v1.0_fasta/scores/S22A1_HUMAN_Yee_2023_activity.csv\n",
      "Scoring SAV1_MOUSE_Tsuboyama_2023_2YSB, rs = 0.5213, saved to ../proteingym_v1.0_fasta/scores/SAV1_MOUSE_Tsuboyama_2023_2YSB.csv\n",
      "Scoring SBI_STAAM_Tsuboyama_2023_2JVG, rs = 0.5969, saved to ../proteingym_v1.0_fasta/scores/SBI_STAAM_Tsuboyama_2023_2JVG.csv\n",
      "Scoring SC6A4_HUMAN_Young_2021, rs = 0.5446, saved to ../proteingym_v1.0_fasta/scores/SC6A4_HUMAN_Young_2021.csv\n",
      "Scoring SCIN_STAAR_Tsuboyama_2023_2QFF, rs = 0.5555, saved to ../proteingym_v1.0_fasta/scores/SCIN_STAAR_Tsuboyama_2023_2QFF.csv\n",
      "Scoring SCN5A_HUMAN_Glazer_2019, rs = 0.1451, saved to ../proteingym_v1.0_fasta/scores/SCN5A_HUMAN_Glazer_2019.csv\n",
      "Scoring SDA_BACSU_Tsuboyama_2023_1PV0, rs = 0.6490, saved to ../proteingym_v1.0_fasta/scores/SDA_BACSU_Tsuboyama_2023_1PV0.csv\n",
      "Scoring SERC_HUMAN_Xie_2023, rs = 0.5703, saved to ../proteingym_v1.0_fasta/scores/SERC_HUMAN_Xie_2023.csv\n",
      "Scoring SHOC2_HUMAN_Kwon_2022, rs = 0.4433, saved to ../proteingym_v1.0_fasta/scores/SHOC2_HUMAN_Kwon_2022.csv\n",
      "Scoring SOX30_HUMAN_Tsuboyama_2023_7JJK, rs = 0.3992, saved to ../proteingym_v1.0_fasta/scores/SOX30_HUMAN_Tsuboyama_2023_7JJK.csv\n",
      "Scoring SPA_STAAU_Tsuboyama_2023_1LP1, rs = 0.3954, saved to ../proteingym_v1.0_fasta/scores/SPA_STAAU_Tsuboyama_2023_1LP1.csv\n",
      "Scoring SPG1_STRSG_Olson_2014, rs = 0.5044, saved to ../proteingym_v1.0_fasta/scores/SPG1_STRSG_Olson_2014.csv\n",
      "Scoring SPG1_STRSG_Wu_2016, rs = 0.2860, saved to ../proteingym_v1.0_fasta/scores/SPG1_STRSG_Wu_2016.csv\n",
      "Scoring SPG2_STRSG_Tsuboyama_2023_5UBS, rs = 0.6736, saved to ../proteingym_v1.0_fasta/scores/SPG2_STRSG_Tsuboyama_2023_5UBS.csv\n",
      "Scoring SPIKE_SARS2_Starr_2020_binding, rs = 0.2817, saved to ../proteingym_v1.0_fasta/scores/SPIKE_SARS2_Starr_2020_binding.csv\n",
      "Scoring SPIKE_SARS2_Starr_2020_expression, rs = 0.1871, saved to ../proteingym_v1.0_fasta/scores/SPIKE_SARS2_Starr_2020_expression.csv\n",
      "Scoring SPTN1_CHICK_Tsuboyama_2023_1TUD, rs = 0.7384, saved to ../proteingym_v1.0_fasta/scores/SPTN1_CHICK_Tsuboyama_2023_1TUD.csv\n",
      "Scoring SQSTM_MOUSE_Tsuboyama_2023_2RRU, rs = 0.7057, saved to ../proteingym_v1.0_fasta/scores/SQSTM_MOUSE_Tsuboyama_2023_2RRU.csv\n",
      "Scoring SR43C_ARATH_Tsuboyama_2023_2N88, rs = 0.7392, saved to ../proteingym_v1.0_fasta/scores/SR43C_ARATH_Tsuboyama_2023_2N88.csv\n",
      "Scoring SRBS1_HUMAN_Tsuboyama_2023_2O2W, rs = 0.7958, saved to ../proteingym_v1.0_fasta/scores/SRBS1_HUMAN_Tsuboyama_2023_2O2W.csv\n",
      "Scoring SRC_HUMAN_Ahler_2019, rs = 0.6036, saved to ../proteingym_v1.0_fasta/scores/SRC_HUMAN_Ahler_2019.csv\n",
      "Scoring SRC_HUMAN_Chakraborty_2023_binding-DAS_25uM, rs = 0.5096, saved to ../proteingym_v1.0_fasta/scores/SRC_HUMAN_Chakraborty_2023_binding-DAS_25uM.csv\n",
      "Scoring SRC_HUMAN_Nguyen_2022, rs = 0.5095, saved to ../proteingym_v1.0_fasta/scores/SRC_HUMAN_Nguyen_2022.csv\n",
      "Scoring SUMO1_HUMAN_Weile_2017, rs = 0.5758, saved to ../proteingym_v1.0_fasta/scores/SUMO1_HUMAN_Weile_2017.csv\n",
      "Scoring SYUA_HUMAN_Newberry_2020, rs = 0.2672, saved to ../proteingym_v1.0_fasta/scores/SYUA_HUMAN_Newberry_2020.csv\n",
      "Scoring TADBP_HUMAN_Bolognesi_2019, rs = 0.0256, saved to ../proteingym_v1.0_fasta/scores/TADBP_HUMAN_Bolognesi_2019.csv\n",
      "Scoring TAT_HV1BR_Fernandes_2016, rs = 0.2341, saved to ../proteingym_v1.0_fasta/scores/TAT_HV1BR_Fernandes_2016.csv\n",
      "Scoring TCRG1_MOUSE_Tsuboyama_2023_1E0L, rs = 0.7526, saved to ../proteingym_v1.0_fasta/scores/TCRG1_MOUSE_Tsuboyama_2023_1E0L.csv\n",
      "Scoring THO1_YEAST_Tsuboyama_2023_2WQG, rs = 0.5689, saved to ../proteingym_v1.0_fasta/scores/THO1_YEAST_Tsuboyama_2023_2WQG.csv\n",
      "Scoring TNKS2_HUMAN_Tsuboyama_2023_5JRT, rs = 0.5844, saved to ../proteingym_v1.0_fasta/scores/TNKS2_HUMAN_Tsuboyama_2023_5JRT.csv\n",
      "Scoring TPK1_HUMAN_Weile_2017, rs = 0.3050, saved to ../proteingym_v1.0_fasta/scores/TPK1_HUMAN_Weile_2017.csv\n",
      "Scoring TPMT_HUMAN_Matreyek_2018, rs = 0.5736, saved to ../proteingym_v1.0_fasta/scores/TPMT_HUMAN_Matreyek_2018.csv\n",
      "Scoring TPOR_HUMAN_Bridgford_2020, rs = 0.3957, saved to ../proteingym_v1.0_fasta/scores/TPOR_HUMAN_Bridgford_2020.csv\n",
      "Scoring TRPC_SACS2_Chan_2017, rs = 0.6715, saved to ../proteingym_v1.0_fasta/scores/TRPC_SACS2_Chan_2017.csv\n",
      "Scoring TRPC_THEMA_Chan_2017, rs = 0.5155, saved to ../proteingym_v1.0_fasta/scores/TRPC_THEMA_Chan_2017.csv\n",
      "Scoring UBC9_HUMAN_Weile_2017, rs = 0.5197, saved to ../proteingym_v1.0_fasta/scores/UBC9_HUMAN_Weile_2017.csv\n",
      "Scoring UBE4B_HUMAN_Tsuboyama_2023_3L1X, rs = 0.5142, saved to ../proteingym_v1.0_fasta/scores/UBE4B_HUMAN_Tsuboyama_2023_3L1X.csv\n",
      "Scoring UBE4B_MOUSE_Starita_2013, rs = 0.4537, saved to ../proteingym_v1.0_fasta/scores/UBE4B_MOUSE_Starita_2013.csv\n",
      "Scoring UBR5_HUMAN_Tsuboyama_2023_1I2T, rs = 0.5751, saved to ../proteingym_v1.0_fasta/scores/UBR5_HUMAN_Tsuboyama_2023_1I2T.csv\n",
      "Scoring VG08_BPP22_Tsuboyama_2023_2GP8, rs = 0.6440, saved to ../proteingym_v1.0_fasta/scores/VG08_BPP22_Tsuboyama_2023_2GP8.csv\n",
      "Scoring VILI_CHICK_Tsuboyama_2023_1YU5, rs = 0.7232, saved to ../proteingym_v1.0_fasta/scores/VILI_CHICK_Tsuboyama_2023_1YU5.csv\n",
      "Scoring VKOR1_HUMAN_Chiasson_2020_abundance, rs = 0.5842, saved to ../proteingym_v1.0_fasta/scores/VKOR1_HUMAN_Chiasson_2020_abundance.csv\n",
      "Scoring VKOR1_HUMAN_Chiasson_2020_activity, rs = 0.4357, saved to ../proteingym_v1.0_fasta/scores/VKOR1_HUMAN_Chiasson_2020_activity.csv\n",
      "Scoring VRPI_BPT7_Tsuboyama_2023_2WNM, rs = 0.6961, saved to ../proteingym_v1.0_fasta/scores/VRPI_BPT7_Tsuboyama_2023_2WNM.csv\n",
      "Scoring YAIA_ECOLI_Tsuboyama_2023_2KVT, rs = 0.6362, saved to ../proteingym_v1.0_fasta/scores/YAIA_ECOLI_Tsuboyama_2023_2KVT.csv\n",
      "Scoring YAP1_HUMAN_Araya_2012, rs = 0.5000, saved to ../proteingym_v1.0_fasta/scores/YAP1_HUMAN_Araya_2012.csv\n",
      "Scoring YNZC_BACSU_Tsuboyama_2023_2JVD, rs = 0.6887, saved to ../proteingym_v1.0_fasta/scores/YNZC_BACSU_Tsuboyama_2023_2JVD.csv\n"
     ]
    }
   ],
   "source": [
    "for file in sequence_folder.glob(\"*.fasta\"):\n",
    "    stem = file.stem\n",
    "    df = score(file, mutant_folder / f\"{stem}.csv\")\n",
    "    df.to_csv(output_folder / f\"{stem}.csv\", index=False)\n",
    "    print(f\"Scoring {stem}, rs = {spearmanr(df['score'], df['predict_score']).correlation:.4f}, saved to {output_folder / f'{stem}.csv'}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "plm",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
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   "nbconvert_exporter": "python",
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