diff options
| -rw-r--r-- | gn3/computations/correlations.py | 3 | ||||
| -rw-r--r-- | gn3/computations/partial_correlations.py | 10 |
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( |