Baseline code review#98

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ElainW wants to merge 21 commits intoOATML-Markslab:mainfrom

ElainW:baseline_code_review

Commits on Feb 10, 2026

refactor the code to take in input as other models in PG

Yilan Wang
authored and
Yilan Wang
committed
enable reading in multi-line fastas

Yilan Wang
authored and
Yilan Wang
committed
add print statement for num sequences and weights dim for debugging

Yilan Wang
authored and
Yilan Wang
committed
change weights_calc_method default to eve, simplify seq_name_to_sequence generaetion

Yilan Wang
authored and
Yilan Wang
committed

Commits on Feb 11, 2026

add directory to paths, update target sequence and MSA filepath input

Yilan Wang
authored and
Yilan Wang
committed
add options to input DMS_index, comment out code to calculate VespaG_Spearman_per_DMS.csv

Yilan Wang
authored and
Yilan Wang
committed
add a check of pdb file suffixes

Yilan Wang
authored and
Yilan Wang
committed
add another error message printout for debugging

Yilan Wang
authored and
Yilan Wang
committed
add options to input DMS_index

Yilan Wang
authored and
Yilan Wang
committed
update ref file input fields

Yilan Wang
authored and
Yilan Wang
committed
fix import path

Yilan Wang
authored and
Yilan Wang
committed
update ref file input fields (target_aa_seq), update the way to access a pandas row

Yilan Wang
authored and
Yilan Wang
committed
update ref file input fields (target_aa_seq and pdb_range)

Yilan Wang
authored and
Yilan Wang
committed
add import path, update ref file input fields target_aa_seq, add comment on MSA_threshold_focus_cols_frac_gaps

Yilan Wang
authored and
Yilan Wang
committed
remove old gemme compute_fitness script as the GEMME docker doesn't have pandas lib

Yilan Wang
authored and
Yilan Wang
committed
add new gemme compute_fitness scripts to accommodate preprocessing and postprocessing using pandas lib when using the docker

Yilan Wang
authored and
Yilan Wang
committed
update progen3 scoring: generate a score.csv for each assay and calculate Spearman after all scoring is completed

Yilan Wang
authored and
Yilan Wang
committed
update names of scripts used

Yilan Wang
authored and
Yilan Wang
committed
update ref file input fields target_aa_seq

Yilan Wang
authored and
Yilan Wang
committed
enable scoring assays through a ref file and DMS indices

Yilan Wang
authored and
Yilan Wang
committed
enable scoring assays through a ref file and DMS indices

Yilan Wang
authored and
Yilan Wang
committed

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Baseline code review#98

Baseline code review#98
ElainW wants to merge 21 commits intoOATML-Markslab:mainfrom
ElainW:baseline_code_review

Commits on Feb 10, 2026

refactor the code to take in input as other models in PG

enable reading in multi-line fastas

add print statement for num sequences and weights dim for debugging

change weights_calc_method default to eve, simplify seq_name_to_sequence generaetion

Commits on Feb 11, 2026

add directory to paths, update target sequence and MSA filepath input

add options to input DMS_index, comment out code to calculate VespaG_Spearman_per_DMS.csv

add a check of pdb file suffixes

add another error message printout for debugging

add options to input DMS_index

update ref file input fields

fix import path

update ref file input fields (target_aa_seq), update the way to access a pandas row

update ref file input fields (target_aa_seq and pdb_range)

add import path, update ref file input fields target_aa_seq, add comment on MSA_threshold_focus_cols_frac_gaps

remove old gemme compute_fitness script as the GEMME docker doesn't have pandas lib

add new gemme compute_fitness scripts to accommodate preprocessing and postprocessing using pandas lib when using the docker

update progen3 scoring: generate a score.csv for each assay and calculate Spearman after all scoring is completed

update names of scripts used

update ref file input fields target_aa_seq

enable scoring assays through a ref file and DMS indices

enable scoring assays through a ref file and DMS indices