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authorFrederick Muriuki Muriithi2021-10-26 09:17:52 +0300
committerFrederick Muriuki Muriithi2021-10-26 09:17:52 +0300
commit39493a3e6b381bc94b54b48657b1f2ac829e4bb2 (patch)
tree21d6da6691d5b4e6703fb04fdb4b4764e1c25b23 /gn3
parentb7c77e2e846a6ddcf308fef5dfb9941f44d6e72a (diff)
downloadgenenetwork3-39493a3e6b381bc94b54b48657b1f2ac829e4bb2.tar.gz
Complete `correlations_of_all_tissue_traits`
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Complete the implementation of the `correlations_of_all_tissue_traits` function by providing a call to a non-implemented function.
Diffstat (limited to 'gn3')
-rw-r--r--gn3/db/correlations.py22
1 files changed, 18 insertions, 4 deletions
diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py
index cae8080..f43b8a5 100644
--- a/gn3/db/correlations.py
+++ b/gn3/db/correlations.py
@@ -265,7 +265,6 @@ 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:
@@ -282,12 +281,25 @@ def fetch_gene_symbol_tissue_value_dict_for_trait(
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.CorrelationPage.calculateCorrOfAllTissueTrait`
+ `web.webqtl.correlation.correlationFunction.calculateCorrOfAllTissueTrait`
function in GeneNetwork1.
"""
- raise Exception("Unimplemented!!!")
- return ({}, {})
+ 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,
@@ -298,6 +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 ""