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authorFrederick Muriuki Muriithi2021-10-29 06:59:57 +0300
committerFrederick Muriuki Muriithi2021-10-29 06:59:57 +0300
commit3609a2d734bfc259ad29b865a9cb45d57124670a (patch)
treec80f3527f8b88b552d100ea3c37beb009313f5cc /gn3
parent7681d1f54b6de2f2e44088e192a51582f34dc669 (diff)
downloadgenenetwork3-3609a2d734bfc259ad29b865a9cb45d57124670a.tar.gz
Move `correlations_of_all_tissue_traits`
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: new function (`correlations_of_all_tissue_traits`). * gn3/db/correlations.py: delete function (`correlations_of_all_tissue_traits`). Move the function to `gn3.computations.partial_correlations` module and comment out the db-access code. Rework it to receive, as arguments, the data it previously fetched from the database, and add comments on future rework to get the function working again.
Diffstat (limited to 'gn3')
-rw-r--r--gn3/computations/partial_correlations.py27
-rw-r--r--gn3/db/correlations.py20
2 files changed, 27 insertions, 20 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index e73edfd..4ba2ba4 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -157,3 +157,30 @@ def batch_computed_tissue_correlation(
`web.webqtl.correlation.correlationFunction.batchCalTissueCorr`"""
raise Exception("Not implemented!")
return ({}, {})
+
+def correlations_of_all_tissue_traits(
+ primary_trait_symbol_value_dict: dict, symbol_value_dict: dict,
+ method: str) -> 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.
+ """
+ # 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 f43b8a5..39ed499 100644
--- a/gn3/db/correlations.py
+++ b/gn3/db/correlations.py
@@ -281,26 +281,6 @@ 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.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,
return_number: int, conn: Any) -> str: