diff options
| -rw-r--r-- | gn3/computations/partial_correlations.py | 13 | ||||
| -rw-r--r-- | gn3/db/correlations.py | 36 |
2 files changed, 33 insertions, 16 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index d095185..5777a0b 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -173,19 +173,6 @@ def correlations_of_all_tissue_traits( `web.webqtl.correlation.correlationFunction.calculateCorrOfAllTissueTrait` function in GeneNetwork1. """ - # The section below existed in the original function, but with the migration - # and the proposed rework (in the near future), the values from the database - # should be passed into this function, rather than have the function fetch - # the data for itself. - # --------------------------------------------------- - # primary_trait_symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait( - # (trait_symbol,), probeset_freeze_id, conn) - # primary_trait_values = primary_trait_symbol_value_dict.vlaues()[0] - # symbol_value_dict = fetch_gene_symbol_tissue_value_dict_for_trait( - # tuple(), probeset_freeze_id, conn) - # --------------------------------------------------- - # We might end up actually getting rid of this function all together as the - # rework is done. primary_trait_values = primary_trait_symbol_value_dict.values()[0] return batch_computed_tissue_correlation( primary_trait_values, symbol_value_dict, method) diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py index 39ed499..28f050a 100644 --- a/gn3/db/correlations.py +++ b/gn3/db/correlations.py @@ -290,10 +290,40 @@ def build_temporary_tissue_correlations_table( This is a migration of the `web.webqtl.correlation.CorrelationPage.getTempTissueCorrTable` function in GeneNetwork1.""" + # We should probably pass the `correlations_of_all_tissue_traits` function + # as an argument to this function and get rid of the two lines immediately + # following this comment. + from gn3.computations.partial_correlations import correlations_of_all_tissue_traits symbol_corr_dict, symbol_p_value_dict = correlations_of_all_tissue_traits( - trait_symbol, probeset_freeze_id, method, conn) - raise Exception("Unimplemented!!!") - return "" + fetch_gene_symbol_tissue_value_dict_for_trait( + (trait_symbol,), probeset_freeze_id, conn), + fetch_gene_symbol_tissue_value_dict_for_trait( + tuple(), probeset_freeze_id, conn), + method) + + symbol_corr_list = sorted( + symbol_corr_dict.items(), + key=compare_tissue_correlation_absolute_values) + + temp_table_name = f"TOPTISSUE{random_string(8)}" + create_query = ( + "CREATE TEMPORARY TABLE {temp_table_name}" + "(Symbol varchar(100) PRIMARY KEY, Correlation float, PValue float)") + insert_query = ( + f"INSERT INTO {temp_table_name}(Symbol, Correlation, PValue) " + " VALUES (%(symbol)s, %(correlation)s, %(pvalue)s)") + + with conn.cursor() as cursor: + cursor.execute(create_query) + cursor.execute( + insert_query, + tuple({ + "symbol": symbol, + "correlation": corr, + "pvalue": symbol_p_value_dict[symbol] + } for symbol, corr in symbol_corr_list[0: 2 * return_number])) + + return temp_table_name def fetch_tissue_correlations( dataset: dict, trait_symbol: str, probeset_freeze_id: int, method: str, |