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zero_shot_config.sh
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zero_shot_config.sh
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# This file has all general filepaths and directories used in the scoring pipeline. The individual scripts may have
# additional parameters specific to each method
# DMS zero-shot parameters
# Folders containing the csvs with the variants for each DMS assay
export DMS_data_folder_subs="Folder containing DMS substitution csvs"
export DMS_data_folder_indels="Folder containing DMS indel csvs"
# Folders containing multiple sequence alignments and MSA weights for all DMS assays
export DMS_MSA_data_folder="folder containing DMS MSA files"
export DMS_MSA_weights_folder="folder containing DMS MSA weights"
# Reference files for substitution and indel assays
export DMS_reference_file_path_subs=../../reference_files/DMS_substitutions.csv
export DMS_reference_file_path_indels=../../reference_files/DMS_indels.csv
# Folders where fitness predictions for baseline models are saved
export DMS_output_score_folder_subs="folder for DMS substitution scores"
export DMS_output_score_folder_indels="folder for DMS indel scores"
# Folder containing EVE models for each DMS assay
export DMS_EVE_model_folder="folder for DMS assay specific EVE models"
# Folders containing merged score files for each DMS assay
export DMS_merged_score_folder_subs="folder for merged scores for DMS substitutions"
export DMS_merged_score_folder_indels="folder for merged score for DMS indels"
# Folders containing predicted structures for the DMSs
export DMS_structure_folder="folder containing predicted structures for each DMS assay"
# Clinical parameters
# Folder containing variant csvs
export clinical_data_folder_subs="folder containing clinical substitution csvs"
export clinical_data_folder_indels="folder containing clinical indel csvs"
# Folders containing multiple sequence alignments and MSA weights for all clinical datasets
export clinical_MSA_data_folder_subs="folder containing clinical MSA files for substitutions"
export clinical_MSA_data_folder_indels="folder containing clinical MSA files for indels"
# Folder containing MSA weights for all clinical datasets
export clinical_MSA_weights_folder_subs="folder containing clinical MSA weights for substitutions"
export clinical_MSA_weights_folder_indels="folder containing clinical MSA weights for indels"
# reference files for substitution and indel clinical variants
export clinical_reference_file_path_subs=../../reference_files/clinical_substitutions.csv
export clinical_reference_file_path_indels=../../reference_files/clinical_indels.csv
# Folder where clinical benchmark fitness predictions for baseline models are saved
export clinical_output_score_folder_subs="folder for clinical substitution scores"
export clinical_output_score_folder_indels="folder for clinical indel scores"
# Folder containing EVE models for each clinical variant
export clinical_EVE_model_folder="folder for clinical EVE models"
# Folder containing merged score files for each clinical variant
export clinical_merged_score_folder_subs="folder for merged scores for clinical substitutions"
export clinical_merged_score_folder_indels="folder for merged score for clinical indels"