diff options
| -rw-r--r-- | gn3/db/species.py | 31 | ||||
| -rw-r--r-- | gn3/partial_correlations.py | 38 | ||||
| -rw-r--r-- | tests/unit/test_partial_correlations.py | 64 |
3 files changed, 130 insertions, 3 deletions
diff --git a/gn3/db/species.py b/gn3/db/species.py index 0deae4e..1e5015f 100644 --- a/gn3/db/species.py +++ b/gn3/db/species.py @@ -30,3 +30,34 @@ def get_chromosome(name: str, is_species: bool, conn: Any) -> Optional[Tuple]: with conn.cursor() as cursor: cursor.execute(_sql) return cursor.fetchall() + +def translate_to_mouse_gene_id(species: str, geneid: int, conn: Any) -> int: + """ + Translate rat or human geneid to mouse geneid + + This is a migration of the + `web.webqtl.correlation/CorrelationPage.translateToMouseGeneID` function in + GN1 + """ + assert species in ("rat", "mouse", "human"), "Invalid species" + if geneid is None: + return 0 + + if species == "mouse": + 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] + + return 0 # default if all else fails diff --git a/gn3/partial_correlations.py b/gn3/partial_correlations.py index c556d10..1fb0ccc 100644 --- a/gn3/partial_correlations.py +++ b/gn3/partial_correlations.py @@ -6,7 +6,7 @@ GeneNetwork1. """ from functools import reduce -from typing import Any, Sequence +from typing import Any, Tuple, Sequence def control_samples(controls: Sequence[dict], sampleslist: Sequence[str]): """ @@ -86,3 +86,39 @@ def fix_samples(primary_trait: dict, control_traits: Sequence[dict]) -> Sequence control_vals_vars[0], tuple(primary_trait[sample]["variance"] for sample in primary_samples), control_vals_vars[1]) + +def find_identical_traits( + primary_name: str, primary_value: float, control_names: Tuple[str, ...], + control_values: Tuple[float, ...]) -> Tuple[str, ...]: + """ + Find traits that have the same value when the values are considered to + 3 decimal places. + + This is a migration of the + `web.webqtl.correlation.correlationFunction.findIdenticalTraits` function in + GN1. + """ + def __merge_identicals__( + acc: Tuple[str, ...], + ident: Tuple[str, Tuple[str, ...]]) -> Tuple[str, ...]: + return acc + ident[1] + + def __dictify_controls__(acc, control_item): + ckey = "{:.3f}".format(control_item[0]) + return {**acc, ckey: acc.get(ckey, tuple()) + (control_item[1],)} + + return (reduce(## for identical control traits + __merge_identicals__, + (item for item in reduce(# type: ignore[var-annotated] + __dictify_controls__, zip(control_values, control_names), + {}).items() if len(item[1]) > 1), + tuple()) + or + reduce(## If no identical control traits, try primary and controls + __merge_identicals__, + (item for item in reduce(# type: ignore[var-annotated] + __dictify_controls__, + zip((primary_value,) + control_values, + (primary_name,) + control_names), {}).items() + if len(item[1]) > 1), + tuple())) diff --git a/tests/unit/test_partial_correlations.py b/tests/unit/test_partial_correlations.py index 7631a71..60e54c1 100644 --- a/tests/unit/test_partial_correlations.py +++ b/tests/unit/test_partial_correlations.py @@ -4,7 +4,8 @@ from unittest import TestCase from gn3.partial_correlations import ( fix_samples, control_samples, - dictify_by_samples) + dictify_by_samples, + find_identical_traits) sampleslist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] control_traits = ( @@ -106,6 +107,8 @@ class TestPartialCorrelations(TestCase): def test_dictify_by_samples(self): """ + Test that `dictify_by_samples` generates the appropriate dict + Given: a sequence of sequences with sample names, values and variances, as in the output of `gn3.partial_correlations.control_samples` or @@ -133,7 +136,34 @@ class TestPartialCorrelations(TestCase): dictified_control_samples) def test_fix_samples(self): - """Test that fix_samples fixes the values""" + """ + Test that `fix_samples` returns only the common samples + + Given: + - A primary trait + - A sequence of control samples + When: + - The two arguments are passed to `fix_samples` + Then: + - Only the names of the samples present in the primary trait that + are also present in ALL the control traits are present in the + return value + - Only the values of the samples present in the primary trait that + are also present in ALL the control traits are present in the + return value + - ALL the values for ALL the control traits are present in the + return value + - Only the variances of the samples present in the primary trait + that are also present in ALL the control traits are present in the + return value + - ALL the variances for ALL the control traits are present in the + return value + - The return value is a tuple of the above items, in the following + order: + ((sample_names, ...), (primary_trait_values, ...), + (control_traits_values, ...), (primary_trait_variances, ...) + (control_traits_variances, ...)) + """ self.assertEqual( fix_samples( {"B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, @@ -149,3 +179,33 @@ class TestPartialCorrelations(TestCase): (None,), (None, None, None, None, None, None, None, None, None, None, None, None, None))) + + def test_find_identical_traits(self): + """ + Test `gn3.partial_correlations.find_identical_traits`. + + Given: + - the name of a primary trait + - the value of a primary trait + - a sequence of names of control traits + - a sequence of values of control traits + When: + - the arguments above are passed to the `find_identical_traits` + function + Then: + - Return ALL trait names that have the same value when up to three + decimal places are considered + """ + for primn, primv, contn, contv, expected in ( + ("pt", 12.98395, ("ct0", "ct1", "ct2"), + (0.1234, 2.3456, 3.4567), tuple()), + ("pt", 12.98395, ("ct0", "ct1", "ct2"), + (12.98354, 2.3456, 3.4567), ("pt", "ct0")), + ("pt", 12.98395, ("ct0", "ct1", "ct2", "ct3"), + (0.1234, 2.3456, 0.1233, 4.5678), ("ct0", "ct2")) + ): + with self.subTest( + primary_name=primn, primary_value=primv, + control_names=contn, control_values=contv): + self.assertEqual( + find_identical_traits(primn, primv, contn, contv), expected) |