Skip to content

Commit

Permalink
cleanup and update
Browse files Browse the repository at this point in the history
  • Loading branch information
matsen committed Jun 6, 2024
1 parent 8195ca6 commit 5f90930
Show file tree
Hide file tree
Showing 2 changed files with 6 additions and 4 deletions.
2 changes: 0 additions & 2 deletions netam/dnsm.py
Original file line number Diff line number Diff line change
Expand Up @@ -186,8 +186,6 @@ def load_branch_lengths(self, in_csv_path):
self.branch_lengths = pd.read_csv(in_csv_path)["branch_length"].values

def update_neutral_aa_mut_probs(self):
print("consolidating neutral rates into substitution probabilities...")

neutral_aa_mut_prob_l = []

for nt_parent, mask, rates, branch_length, subs_probs in zip(
Expand Down
8 changes: 6 additions & 2 deletions tests/test_dnsm.py
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,8 @@
from netam.framework import (
crepe_exists,
load_crepe,
load_and_add_shm_model_outputs_to_pcp_df,
load_pcp_df,
add_shm_model_outputs_to_pcp_df,
)
from netam.common import aa_idx_tensor_of_str_ambig, MAX_AMBIG_AA_IDX
from netam.models import TransformerBinarySelectionModelWiggleAct
Expand All @@ -22,8 +23,11 @@ def test_aa_idx_tensor_of_str_ambig():

@pytest.fixture
def pcp_df():
df = load_and_add_shm_model_outputs_to_pcp_df(
df = load_pcp_df(
"data/wyatt-10x-1p5m_pcp_2023-11-30_NI.first100.csv.gz",
)
df = add_shm_model_outputs_to_pcp_df(
df,
"data/cnn_joi_sml-shmoof_small",
)
return df
Expand Down

0 comments on commit 5f90930

Please sign in to comment.