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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
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.
-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: