diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/computations/partial_correlations.py (renamed from gn3/partial_correlations.py) | 35 | ||||
| -rw-r--r-- | gn3/db/correlations.py | 37 | ||||
| -rw-r--r-- | gn3/db/species.py | 20 |
3 files changed, 76 insertions, 16 deletions
diff --git a/gn3/partial_correlations.py b/gn3/computations/partial_correlations.py index 1fb0ccc..e73edfd 100644 --- a/gn3/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -7,6 +7,7 @@ GeneNetwork1. from functools import reduce from typing import Any, Tuple, Sequence +from scipy.stats import pearsonr, spearmanr def control_samples(controls: Sequence[dict], sampleslist: Sequence[str]): """ @@ -122,3 +123,37 @@ def find_identical_traits( (primary_name,) + control_names), {}).items() if len(item[1]) > 1), tuple())) + +def tissue_correlation( + primary_trait_values: Tuple[float, ...], + target_trait_values: Tuple[float, ...], + method: str) -> Tuple[float, float]: + """ + Compute the correlation between the primary trait values, and the values of + a single target value. + + This migrates the `cal_tissue_corr` function embedded in the larger + `web.webqtl.correlation.correlationFunction.batchCalTissueCorr` function in + GeneNetwork1. + """ + def spearman_corr(*args): + result = spearmanr(*args) + return (result.correlation, result.pvalue) + + method_fns = {"pearson": pearsonr, "spearman": spearman_corr} + + assert len(primary_trait_values) == len(target_trait_values), ( + "The lengths of the `primary_trait_values` and `target_trait_values` " + "must be equal") + assert method in method_fns.keys(), ( + "Method must be one of: {}".format(",".join(method_fns.keys()))) + + return method_fns[method](primary_trait_values, target_trait_values) + +def batch_computed_tissue_correlation( + trait_value: str, symbol_value_dict: dict, + method: str = "pearson") -> Tuple[dict, dict]: + """ + `web.webqtl.correlation.correlationFunction.batchCalTissueCorr`""" + raise Exception("Not implemented!") + return ({}, {}) diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py index 87ab082..f43b8a5 100644 --- a/gn3/db/correlations.py +++ b/gn3/db/correlations.py @@ -265,14 +265,41 @@ def fetch_tissue_probeset_xref_info( results or tuple(), (tuple(), {}, {}, {}, {}, {}, {})) -def correlations_of_all_tissue_traits() -> Tuple[dict, dict]: +def fetch_gene_symbol_tissue_value_dict_for_trait( + gene_name_list: Tuple[str, ...], probeset_freeze_id: int, + conn: Any) -> dict: """ + Fetches a map of the gene symbols to the tissue values. + This is a migration of the - `web.webqtl.correlation.CorrelationPage.calculateCorrOfAllTissueTrait` + `web.webqtl.correlation.correlationFunction.getGeneSymbolTissueValueDictForTrait` function in GeneNetwork1. """ - raise Exception("Unimplemented!!!") - return ({}, {}) + xref_info = fetch_tissue_probeset_xref_info( + gene_name_list, probeset_freeze_id, conn) + if xref_info[0]: + return fetch_gene_symbol_tissue_value_dict(xref_info[0], xref_info[2], conn) + return {} + +def correlations_of_all_tissue_traits( + trait_symbol: str, probeset_freeze_id: int, + method: str, conn: Any) -> Tuple[dict, dict]: + """ + Computes and returns the correlation of all tissue traits. + + This is a migration of the + `web.webqtl.correlation.correlationFunction.calculateCorrOfAllTissueTrait` + function in GeneNetwork1. + """ + primary_trait_symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait( + (trait_symbol,), probeset_freeze_id, conn) + primary_trait_value = primary_trait_symbol_value_dict.vlaues()[0] + symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait( + tuple(), probeset_freeze_id, conn) + if method == "1": + return batch_computed_tissue_correlation( + primaryTraitValue,SymbolValueDict,method='spearman') + return batch_computed_tissue_correlation(primaryTraitValue,SymbolValueDict) def build_temporary_tissue_correlations_table( trait_symbol: str, probeset_freeze_id: int, method: str, @@ -283,6 +310,8 @@ def build_temporary_tissue_correlations_table( This is a migration of the `web.webqtl.correlation.CorrelationPage.getTempTissueCorrTable` function in GeneNetwork1.""" + symbol_corr_dict, symbol_p_value_dict = correlations_of_all_tissue_traits( + trait_symbol, probeset_freeze_id, method, conn) raise Exception("Unimplemented!!!") return "" diff --git a/gn3/db/species.py b/gn3/db/species.py index 1e5015f..702a9a8 100644 --- a/gn3/db/species.py +++ b/gn3/db/species.py @@ -47,17 +47,13 @@ def translate_to_mouse_gene_id(species: str, geneid: int, conn: Any) -> int: return geneid with conn.cursor as cursor: - if species == "rat": - cursor.execute( - "SELECT mouse FROM GeneIDXRef WHERE rat = %s", geneid) - rat_geneid = cursor.fetchone() - if rat_geneid: - return rat_geneid[0] - - cursor.execute( - "SELECT mouse FROM GeneIDXRef WHERE human = %s", geneid) - human_geneid = cursor.fetchone() - if human_geneid: - return human_geneid[0] + query = { + "rat": "SELECT mouse FROM GeneIDXRef WHERE rat = %s", + "human": "SELECT mouse FROM GeneIDXRef WHERE human = %s" + } + cursor.execute(query[species], geneid) + translated_gene_id = cursor.fetchone() + if translated_gene_id: + return translated_gene_id[0] return 0 # default if all else fails |