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-rw-r--r--gn3/computations/correlations.py3
-rw-r--r--gn3/computations/partial_correlations.py10
2 files changed, 8 insertions, 5 deletions
diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py
index 345b8d7..1b4b3a4 100644
--- a/gn3/computations/correlations.py
+++ b/gn3/computations/correlations.py
@@ -7,6 +7,7 @@ from typing import List
from typing import Tuple
from typing import Optional
from typing import Callable
+from typing import Generator
import scipy.stats
import pingouin as pg
@@ -106,7 +107,7 @@ package :not packaged in guix
def filter_shared_sample_keys(this_samplelist,
- target_samplelist) -> Tuple[List, List]:
+ target_samplelist) -> Generator:
"""Given primary and target sample-list for two base and target trait select
filter the values using the shared keys
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 1e4a646..984c15a 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -217,7 +217,7 @@ def good_dataset_samples_indexes(
def partial_correlations_fast(# pylint: disable=[R0913, R0914]
samples, primary_vals, control_vals, database_filename,
fetched_correlations, method: str, correlation_type: str) -> Tuple[
- float, Tuple[float, ...]]:
+ int, Tuple[float, ...]]:
"""
Computes partial correlation coefficients using data from a CSV file.
@@ -350,7 +350,9 @@ def compute_partial(
def partial_correlations_normal(# pylint: disable=R0913
primary_vals, control_vals, input_trait_gene_id, trait_database,
data_start_pos: int, db_type: str, method: str) -> Tuple[
- float, Tuple[float, ...]]:
+ int, Tuple[Union[
+ Tuple[str, int, float, float, float, float], None],
+ ...]]:#Tuple[float, ...]
"""
Computes the correlation coefficients.
@@ -485,7 +487,7 @@ def literature_correlation_by_list(
def tissue_correlation_by_list(
conn: Any, primary_trait_symbol: str, tissue_probeset_freeze_id: int,
- method: str, trait_list: Tuple[dict]) -> Tuple[dict]:
+ method: str, trait_list: Tuple[dict]) -> Tuple[dict, ...]:
"""
This is a migration of the
`web.webqtl.correlation.CorrelationPage.getTissueCorrelationByList`
@@ -508,7 +510,7 @@ def tissue_correlation_by_list(
primary_trait_value = prim_trait_symbol_value_dict[
primary_trait_symbol.lower()]
gene_symbol_list = tuple(
- trait for trait in trait_list if "symbol" in trait.keys())
+ trait["symbol"] for trait in trait_list if "symbol" in trait.keys())
symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait(
gene_symbol_list, tissue_probeset_freeze_id, conn)
return tuple(