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-rw-r--r--gn3/db/traits.py69
-rw-r--r--gn3/heatmaps.py67
-rw-r--r--tests/unit/db/test_traits.py89
-rw-r--r--tests/unit/test_heatmaps.py87
4 files changed, 159 insertions, 153 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index f2673c8..1e29aff 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -1,12 +1,81 @@
"""This class contains functions relating to trait data manipulation"""
import os
+from functools import reduce
from typing import Any, Dict, Union, Sequence
+
from gn3.settings import TMPDIR
from gn3.random import random_string
from gn3.function_helpers import compose
from gn3.db.datasets import retrieve_trait_dataset
+def export_trait_data(
+ trait_data: dict, samplelist: Sequence[str], dtype: str = "val",
+ var_exists: bool = False, n_exists: bool = False):
+ """
+ Export data according to `samplelist`. Mostly used in calculating
+ correlations.
+
+ DESCRIPTION:
+ Migrated from
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L166-L211
+
+ PARAMETERS
+ trait: (dict)
+ The dictionary of key-value pairs representing a trait
+ samplelist: (list)
+ A list of sample names
+ dtype: (str)
+ ... verify what this is ...
+ var_exists: (bool)
+ A flag indicating existence of variance
+ n_exists: (bool)
+ A flag indicating existence of ndata
+ """
+ def __export_all_types(tdata, sample):
+ sample_data = []
+ if tdata[sample]["value"]:
+ sample_data.append(tdata[sample]["value"])
+ if var_exists:
+ if tdata[sample]["variance"]:
+ sample_data.append(tdata[sample]["variance"])
+ else:
+ sample_data.append(None)
+ if n_exists:
+ if tdata[sample]["ndata"]:
+ sample_data.append(tdata[sample]["ndata"])
+ else:
+ sample_data.append(None)
+ else:
+ if var_exists and n_exists:
+ sample_data += [None, None, None]
+ elif var_exists or n_exists:
+ sample_data += [None, None]
+ else:
+ sample_data.append(None)
+
+ return tuple(sample_data)
+
+ def __exporter(accumulator, sample):
+ # pylint: disable=[R0911]
+ if sample in trait_data["data"]:
+ if dtype == "val":
+ return accumulator + (trait_data["data"][sample]["value"], )
+ if dtype == "var":
+ return accumulator + (trait_data["data"][sample]["variance"], )
+ if dtype == "N":
+ return accumulator + (trait_data["data"][sample]["ndata"], )
+ if dtype == "all":
+ return accumulator + __export_all_types(trait_data["data"], sample)
+ raise KeyError("Type `%s` is incorrect" % dtype)
+ if var_exists and n_exists:
+ return accumulator + (None, None, None)
+ if var_exists or n_exists:
+ return accumulator + (None, None)
+ return accumulator + (None,)
+
+ return reduce(__exporter, samplelist, tuple())
+
def get_trait_csv_sample_data(conn: Any,
trait_name: int, phenotype_id: int):
"""Fetch a trait and return it as a csv string"""
diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py
index adbfbc6..3b94e88 100644
--- a/gn3/heatmaps.py
+++ b/gn3/heatmaps.py
@@ -14,6 +14,7 @@ from plotly.subplots import make_subplots # type: ignore
from gn3.settings import TMPDIR
from gn3.random import random_string
from gn3.computations.slink import slink
+from gn3.db.traits import export_trait_data
from gn3.computations.correlations2 import compute_correlation
from gn3.db.genotypes import (
build_genotype_file, load_genotype_samples)
@@ -26,72 +27,6 @@ from gn3.computations.qtlreaper import (
parse_reaper_main_results,
organise_reaper_main_results)
-def export_trait_data(
- trait_data: dict, samplelist: Sequence[str], dtype: str = "val",
- var_exists: bool = False, n_exists: bool = False):
- """
- Export data according to `samplelist`. Mostly used in calculating
- correlations.
-
- DESCRIPTION:
- Migrated from
- https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L166-L211
-
- PARAMETERS
- trait: (dict)
- The dictionary of key-value pairs representing a trait
- samplelist: (list)
- A list of sample names
- dtype: (str)
- ... verify what this is ...
- var_exists: (bool)
- A flag indicating existence of variance
- n_exists: (bool)
- A flag indicating existence of ndata
- """
- def __export_all_types(tdata, sample):
- sample_data = []
- if tdata[sample]["value"]:
- sample_data.append(tdata[sample]["value"])
- if var_exists:
- if tdata[sample]["variance"]:
- sample_data.append(tdata[sample]["variance"])
- else:
- sample_data.append(None)
- if n_exists:
- if tdata[sample]["ndata"]:
- sample_data.append(tdata[sample]["ndata"])
- else:
- sample_data.append(None)
- else:
- if var_exists and n_exists:
- sample_data += [None, None, None]
- elif var_exists or n_exists:
- sample_data += [None, None]
- else:
- sample_data.append(None)
-
- return tuple(sample_data)
-
- def __exporter(accumulator, sample):
- # pylint: disable=[R0911]
- if sample in trait_data["data"]:
- if dtype == "val":
- return accumulator + (trait_data["data"][sample]["value"], )
- if dtype == "var":
- return accumulator + (trait_data["data"][sample]["variance"], )
- if dtype == "N":
- return accumulator + (trait_data["data"][sample]["ndata"], )
- if dtype == "all":
- return accumulator + __export_all_types(trait_data["data"], sample)
- raise KeyError("Type `%s` is incorrect" % dtype)
- if var_exists and n_exists:
- return accumulator + (None, None, None)
- if var_exists or n_exists:
- return accumulator + (None, None)
- return accumulator + (None,)
-
- return reduce(__exporter, samplelist, tuple())
def trait_display_name(trait: Dict):
"""
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index 8af8e82..0c4ef78 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -2,6 +2,7 @@
from unittest import mock, TestCase
from gn3.db.traits import (
build_trait_name,
+ export_trait_data,
set_haveinfo_field,
update_sample_data,
retrieve_trait_info,
@@ -12,6 +13,38 @@ from gn3.db.traits import (
retrieve_publish_trait_info,
retrieve_probeset_trait_info)
+samplelist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
+trait_data = {
+ "mysqlid": 36688172,
+ "data": {
+ "B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None},
+ "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None},
+ "BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None},
+ "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None},
+ "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None},
+ "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None},
+ "BXD21": {"sample_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None},
+ "BXD24": {"sample_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None},
+ "BXD27": {"sample_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None},
+ "BXD28": {"sample_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None},
+ "BXD32": {"sample_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None},
+ "BXD39": {"sample_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None},
+ "BXD40": {"sample_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None},
+ "BXD42": {"sample_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None},
+ "BXD6": {"sample_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None},
+ "BXH14": {"sample_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None},
+ "BXH19": {"sample_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None},
+ "BXH2": {"sample_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None},
+ "BXH22": {"sample_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None},
+ "BXH4": {"sample_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None},
+ "BXH6": {"sample_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None},
+ "BXH7": {"sample_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None},
+ "BXH8": {"sample_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None},
+ "BXH9": {"sample_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None},
+ "C3H/HeJ": {"sample_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None},
+ "C57BL/6J": {"sample_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None},
+ "DBA/2J": {"sample_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}}
+
class TestTraitsDBFunctions(TestCase):
"Test cases for traits functions"
@@ -226,3 +259,59 @@ class TestTraitsDBFunctions(TestCase):
with self.subTest(trait_info=trait_info, expected=expected):
self.assertEqual(
set_confidential_field(trait_type, trait_info), expected)
+
+ def test_export_trait_data_dtype(self):
+ """
+ Test `export_trait_data` with different values for the `dtype` keyword
+ argument
+ """
+ for dtype, expected in [
+ ["val", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
+ ["var", (None, None, None, None, None, None)],
+ ["N", (None, None, None, None, None, None)],
+ ["all", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)]]:
+ with self.subTest(dtype=dtype):
+ self.assertEqual(
+ export_trait_data(trait_data, samplelist, dtype=dtype),
+ expected)
+
+ def test_export_trait_data_dtype_all_flags(self):
+ """
+ Test `export_trait_data` with different values for the `dtype` keyword
+ argument and the different flags set up
+ """
+ for dtype, vflag, nflag, expected in [
+ ["val", False, False,
+ (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
+ ["val", False, True,
+ (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
+ ["val", True, False,
+ (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
+ ["val", True, True,
+ (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
+ ["var", False, False, (None, None, None, None, None, None)],
+ ["var", False, True, (None, None, None, None, None, None)],
+ ["var", True, False, (None, None, None, None, None, None)],
+ ["var", True, True, (None, None, None, None, None, None)],
+ ["N", False, False, (None, None, None, None, None, None)],
+ ["N", False, True, (None, None, None, None, None, None)],
+ ["N", True, False, (None, None, None, None, None, None)],
+ ["N", True, True, (None, None, None, None, None, None)],
+ ["all", False, False,
+ (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
+ ["all", False, True,
+ (7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
+ 8.30401, None, 7.80944, None)],
+ ["all", True, False,
+ (7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
+ 8.30401, None, 7.80944, None)],
+ ["all", True, True,
+ (7.51879, None, None, 7.77141, None, None, 8.39265, None, None,
+ 8.17443, None, None, 8.30401, None, None, 7.80944, None, None)]
+ ]:
+ with self.subTest(dtype=dtype, vflag=vflag, nflag=nflag):
+ self.assertEqual(
+ export_trait_data(
+ trait_data, samplelist, dtype=dtype, var_exists=vflag,
+ n_exists=nflag),
+ expected)
diff --git a/tests/unit/test_heatmaps.py b/tests/unit/test_heatmaps.py
index 7b66688..03fd4a6 100644
--- a/tests/unit/test_heatmaps.py
+++ b/tests/unit/test_heatmaps.py
@@ -4,43 +4,12 @@ from gn3.heatmaps import (
cluster_traits,
get_loci_names,
get_lrs_from_chr,
- export_trait_data,
compute_traits_order,
retrieve_samples_and_values,
process_traits_data_for_heatmap)
from tests.unit.sample_test_data import organised_trait_1, organised_trait_2
samplelist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
-trait_data = {
- "mysqlid": 36688172,
- "data": {
- "B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None},
- "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None},
- "BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None},
- "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None},
- "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None},
- "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None},
- "BXD21": {"sample_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None},
- "BXD24": {"sample_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None},
- "BXD27": {"sample_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None},
- "BXD28": {"sample_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None},
- "BXD32": {"sample_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None},
- "BXD39": {"sample_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None},
- "BXD40": {"sample_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None},
- "BXD42": {"sample_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None},
- "BXD6": {"sample_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None},
- "BXH14": {"sample_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None},
- "BXH19": {"sample_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None},
- "BXH2": {"sample_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None},
- "BXH22": {"sample_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None},
- "BXH4": {"sample_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None},
- "BXH6": {"sample_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None},
- "BXH7": {"sample_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None},
- "BXH8": {"sample_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None},
- "BXH9": {"sample_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None},
- "C3H/HeJ": {"sample_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None},
- "C57BL/6J": {"sample_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None},
- "DBA/2J": {"sample_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}}
slinked = (
(((0, 2, 0.16381088984330505),
@@ -55,62 +24,6 @@ slinked = (
class TestHeatmap(TestCase):
"""Class for testing heatmap computation functions"""
- def test_export_trait_data_dtype(self):
- """
- Test `export_trait_data` with different values for the `dtype` keyword
- argument
- """
- for dtype, expected in [
- ["val", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
- ["var", (None, None, None, None, None, None)],
- ["N", (None, None, None, None, None, None)],
- ["all", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)]]:
- with self.subTest(dtype=dtype):
- self.assertEqual(
- export_trait_data(trait_data, samplelist, dtype=dtype),
- expected)
-
- def test_export_trait_data_dtype_all_flags(self):
- """
- Test `export_trait_data` with different values for the `dtype` keyword
- argument and the different flags set up
- """
- for dtype, vflag, nflag, expected in [
- ["val", False, False,
- (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
- ["val", False, True,
- (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
- ["val", True, False,
- (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
- ["val", True, True,
- (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
- ["var", False, False, (None, None, None, None, None, None)],
- ["var", False, True, (None, None, None, None, None, None)],
- ["var", True, False, (None, None, None, None, None, None)],
- ["var", True, True, (None, None, None, None, None, None)],
- ["N", False, False, (None, None, None, None, None, None)],
- ["N", False, True, (None, None, None, None, None, None)],
- ["N", True, False, (None, None, None, None, None, None)],
- ["N", True, True, (None, None, None, None, None, None)],
- ["all", False, False,
- (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
- ["all", False, True,
- (7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
- 8.30401, None, 7.80944, None)],
- ["all", True, False,
- (7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
- 8.30401, None, 7.80944, None)],
- ["all", True, True,
- (7.51879, None, None, 7.77141, None, None, 8.39265, None, None,
- 8.17443, None, None, 8.30401, None, None, 7.80944, None, None)]
- ]:
- with self.subTest(dtype=dtype, vflag=vflag, nflag=nflag):
- self.assertEqual(
- export_trait_data(
- trait_data, samplelist, dtype=dtype, var_exists=vflag,
- n_exists=nflag),
- expected)
-
def test_cluster_traits(self):
"""
Test that the clustering is working as expected.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 01:13:26 +0000