aboutsummaryrefslogtreecommitdiff
path: root/gn3
diff options
context:
space:
mode:
Diffstat (limited to 'gn3')
-rw-r--r--gn3/computations/partial_correlations.py (renamed from gn3/partial_correlations.py)70
-rw-r--r--gn3/data_helpers.py14
-rw-r--r--gn3/db/correlations.py109
-rw-r--r--gn3/db/species.py20
4 files changed, 177 insertions, 36 deletions
diff --git a/gn3/partial_correlations.py b/gn3/computations/partial_correlations.py
index 1fb0ccc..ba4de9e 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 +123,72 @@ 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())))
+
+ corr, pvalue = method_fns[method](primary_trait_values, target_trait_values)
+ return (round(corr, 10), round(pvalue, 10))
+
+def batch_computed_tissue_correlation(
+ primary_trait_values: Tuple[float, ...], target_traits_dict: dict,
+ method: str) -> Tuple[dict, dict]:
+ """
+ This is a migration of the
+ `web.webqtl.correlation.correlationFunction.batchCalTissueCorr` function in
+ GeneNetwork1
+ """
+ def __corr__(acc, target):
+ corr = tissue_correlation(primary_trait_values, target[1], method)
+ return ({**acc[0], target[0]: corr[0]}, {**acc[0], target[1]: corr[1]})
+ return reduce(__corr__, target_traits_dict.items(), ({}, {}))
+
+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.
+ """
+ primary_trait_values = tuple(primary_trait_symbol_value_dict.values())[0]
+ return batch_computed_tissue_correlation(
+ primary_trait_values, symbol_value_dict, method)
+
+def good_dataset_samples_indexes(
+ samples: Tuple[str, ...],
+ samples_from_file: Tuple[str, ...]) -> Tuple[int, ...]:
+ """
+ Return the indexes of the items in `samples_from_files` that are also found
+ in `samples`.
+
+ This is a partial migration of the
+ `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast`
+ function in GeneNetwork1.
+ """
+ return tuple(sorted(
+ samples_from_file.index(good) for good in
+ set(samples).intersection(set(samples_from_file))))
diff --git a/gn3/data_helpers.py b/gn3/data_helpers.py
index f0d971e..d3f942b 100644
--- a/gn3/data_helpers.py
+++ b/gn3/data_helpers.py
@@ -5,7 +5,7 @@ data structures.
from math import ceil
from functools import reduce
-from typing import Any, Tuple, Sequence
+from typing import Any, Tuple, Sequence, Optional
def partition_all(num: int, items: Sequence[Any]) -> Tuple[Tuple[Any, ...], ...]:
"""
@@ -23,3 +23,15 @@ def partition_all(num: int, items: Sequence[Any]) -> Tuple[Tuple[Any, ...], ...]
tuple(items[start:stop]) for start, stop # type: ignore[has-type]
in reduce(
__compute_start_stop__, iterations, tuple())])
+
+def parse_csv_line(
+ line: str, delimiter: str = ",",
+ quoting: Optional[str] = '"') -> Tuple[str, ...]:
+ """
+ Parses a line from a CSV file into a tuple of strings.
+
+ This is a migration of the `web.webqtl.utility.webqtlUtil.readLineCSV`
+ function in GeneNetwork1.
+ """
+ return tuple(
+ col.strip("{} \t\n".format(quoting)) for col in line.split(delimiter))
diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py
index 87ab082..06b3310 100644
--- a/gn3/db/correlations.py
+++ b/gn3/db/correlations.py
@@ -10,6 +10,8 @@ from gn3.random import random_string
from gn3.data_helpers import partition_all
from gn3.db.species import translate_to_mouse_gene_id
+from gn3.computations.partial_correlations import correlations_of_all_tissue_traits
+
def get_filename(target_db_name: str, conn: Any) -> str:
"""
Retrieve the name of the reference database file with which correlations are
@@ -140,22 +142,6 @@ def fetch_literature_correlations(
cursor.execute("DROP TEMPORARY TABLE %s", temp_table)
return dict(results)
-def compare_tissue_correlation_absolute_values(val1, val2):
- """
- Comparison function for use when sorting tissue correlation values.
-
- This is a partial migration of the
- `web.webqtl.correlation.CorrelationPage.getTempTissueCorrTable` function in
- GeneNetwork1."""
- try:
- if abs(val1) < abs(val2):
- return 1
- if abs(val1) == abs(val2):
- return 0
- return -1
- except TypeError:
- return 0
-
def fetch_symbol_value_pair_dict(
symbol_list: Tuple[str, ...], data_id_dict: dict,
conn: Any) -> Dict[str, Tuple[float, ...]]:
@@ -265,14 +251,21 @@ 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 build_temporary_tissue_correlations_table(
trait_symbol: str, probeset_freeze_id: int, method: str,
@@ -283,10 +276,40 @@ def build_temporary_tissue_correlations_table(
This is a migration of the
`web.webqtl.correlation.CorrelationPage.getTempTissueCorrTable` function in
GeneNetwork1."""
- raise Exception("Unimplemented!!!")
- return ""
+ # We should probably pass the `correlations_of_all_tissue_traits` function
+ # as an argument to this function and get rid of the one call immediately
+ # following this comment.
+ symbol_corr_dict, symbol_p_value_dict = correlations_of_all_tissue_traits(
+ 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=lambda key_val: key_val[1])
+
+ 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)")
-def fetch_tissue_correlations(
+ 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(# pylint: disable=R0913
dataset: dict, trait_symbol: str, probeset_freeze_id: int, method: str,
return_number: int, conn: Any) -> dict:
"""
@@ -316,3 +339,43 @@ def fetch_tissue_correlations(
return {
trait_name: (tiss_corr, tiss_p_val)
for trait_name, tiss_corr, tiss_p_val in results}
+
+def check_for_literature_info(conn: Any, geneid: int) -> bool:
+ """
+ Checks the database to find out whether the trait with `geneid` has any
+ associated literature.
+
+ This is a migration of the
+ `web.webqtl.correlation.CorrelationPage.checkForLitInfo` function in
+ GeneNetwork1.
+ """
+ query = "SELECT 1 FROM LCorrRamin3 WHERE GeneId1=%s LIMIT 1"
+ with conn.cursor() as cursor:
+ cursor.execute(query, geneid)
+ result = cursor.fetchone()
+ if result:
+ return True
+
+ return False
+
+def check_symbol_for_tissue_correlation(
+ conn: Any, tissue_probeset_freeze_id: int, symbol: str = "") -> bool:
+ """
+ Checks whether a symbol has any associated tissue correlations.
+
+ This is a migration of the
+ `web.webqtl.correlation.CorrelationPage.checkSymbolForTissueCorr` function
+ in GeneNetwork1.
+ """
+ query = (
+ "SELECT 1 FROM TissueProbeSetXRef "
+ "WHERE TissueProbeSetFreezeId=%(probeset_freeze_id)s "
+ "AND Symbol=%(symbol)s LIMIT 1")
+ with conn.cursor() as cursor:
+ cursor.execute(
+ query, probeset_freeze_id=tissue_probeset_freeze_id, symbol=symbol)
+ result = cursor.fetchone()
+ if result:
+ return True
+
+ return False
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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 22:51:39 +0000