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Bug fixes for api #316

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Merged
merged 3 commits into from
Jan 31, 2025
Merged

Bug fixes for api #316

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ee973b3
fixed bug where 'split_class' wouldn't be removed from `dataset.exper…
ymahlich Jan 30, 2025
c3c15c7
fixed issue where genes.tsv would not be downloaded if only one speci…
ymahlich Jan 30, 2025
2107ff6
changed orientation of wide format tables returned for omic types 'tr…
ymahlich Jan 31, 2025
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11 changes: 7 additions & 4 deletions coderdata/dataset/dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -494,7 +494,7 @@ def format(
values='transcriptomics',
index='entrez_id',
columns='improve_sample_id'
)
).transpose()

elif data_type == "mutations":
if data.mutations is None:
Expand All @@ -516,7 +516,7 @@ def format(
columns='improve_sample_id',
values='exists',
fill_value=0,
)
).transpose()

elif data_type == "copy_number":
if data.copy_number is None:
Expand All @@ -531,7 +531,7 @@ def format(
columns='improve_sample_id',
values='copy_number',
aggfunc='mean',
)
).transpose()
if copy_call:
ret = ret.apply(
pd.cut,
Expand All @@ -552,7 +552,7 @@ def format(
values='proteomics',
index='entrez_id',
columns='improve_sample_id'
)
).transpose()

elif data_type == "experiments":
if data.experiments is None:
Expand Down Expand Up @@ -936,13 +936,16 @@ def train_test_validate(
sss_1.split(X=df_full, y=df_full['split_class'])
)
df_train = df_full.iloc[idx_train]
df_train = df_train.drop(labels=['split_class'], axis=1)
df_other = df_full.iloc[idx_other]
# Splitting 'other' further into test and validate
idx_test, idx_val = next(
sss_2.split(X=df_other, y=df_other['split_class'])
)
df_test = df_other.iloc[idx_test]
df_test = df_test.drop(labels=['split_class'], axis=1)
df_val = df_other.iloc[idx_val]
df_val = df_val.drop(labels=['split_class'], axis=1)

# using StratifiedGroupKSplit for the stratified drug-/sample-
# blind splits.
Expand Down
2 changes: 1 addition & 1 deletion coderdata/download/downloader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ def download(
file
for file
in data['files']
if file['name'].startswith(name)
if file['name'].startswith(name) or 'genes' in file['name']
]
else:
filtered_files = data['files']
Expand Down