MOI enum

docs/user-guide/python_notebook.md

@@ -8,7 +8,7 @@ The following sections explain how to use Python code to create phenopackets fro
 We first import the TemplateImporter to import the data and create phenopackets, and several classes to visualize the data.
 
 ```python
-from pyphetools.creation import TemplateImporter
+from pyphetools.creation import TemplateImporter, Moi
 from pyphetools.visualization import IndividualTable, QcVisualizer
 from IPython.display import display, HTML
 import pyphetools
@@ -78,11 +78,11 @@ the mode of inheritance (MOI) and then indicate the MOI. If multiple distinct di
 Check results of variant encoding.
 ```python
 pmid = "PMID:36333996"
-timporter.create_hpoa_from_phenopackets(pmid=pmid, moi="Autosomal recessive")
+df = timporter.create_hpoa_from_phenopackets(pmid=pmid, mode_of_inheritance=Moi.AR)
 ```
 or
 
 ```python
 pmid = "PMID:36333996"
-timporter.create_hpoa_from_phenopackets(pmid=pmid, moi="Autosomal recessive", target="OMIM:620427")
+df = timporter.create_hpoa_from_phenopackets(pmid=pmid, mode_of_inheritance=Moi.AD, target="OMIM:620427")
 ```

src/pyphetools/__init__.py

@@ -5,7 +5,7 @@
 from . import validation
 
 
-__version__ = "0.9.92"
+__version__ = "0.9.93"
 
 
 __all__ = [

src/pyphetools/creation/__init__.py

@@ -21,6 +21,7 @@
 from .import_template import TemplateImporter
 from .individual import Individual
 from .metadata import MetaData
+from .mode_of_inheritance import Moi
 from .option_column_mapper import OptionColumnMapper
 from .pyphetools_age import PyPheToolsAge, IsoAge, HpoAge, GestationalAge, HPO_ONSET_TERMS
 from .sex_column_mapper import SexColumnMapper

src/pyphetools/creation/import_template.py

@@ -3,6 +3,7 @@
 from collections import defaultdict
 import typing
 import phenopackets as PPKt
+from .mode_of_inheritance import Moi
 
 
 class TemplateImporter:
@@ -245,15 +246,15 @@ def filter_diseases(disease_id, ppkt_list):
 
     def create_hpoa_from_phenopackets(self,
                                     pmid:str,
-                                    moi:str, 
+                                    mode_of_inheritance:Moi, 
                                     ppkt_dir:str="phenopackets",
                                     target:str=None) -> pd.DataFrame:
         """Create an HPO annotation (HPOA) file from the current cohort
 
         :param pmid: PubMed id for the mode of inheritance
         :type pmid: str
-        :param moi: Mode of inheritance (Autosomal dominant, Autosomal recessive, etc)
-        :type moi: str
+        :param mode_of_inheritance: Mode of inheritance (enumeration)
+        :type mode_of_inheritance: Moi
         :param ppkt_dir: Directory with phenopackets Defaults to "phenopackets".
         :param target: Disease id (e.g., OMIM:600123) to select only phenopackets with this disease. Defaults to None.
         :type target: str
@@ -271,18 +272,7 @@ def create_hpoa_from_phenopackets(self,
             ppkt_list = TemplateImporter.filter_diseases(target, ppkt_list)
         TemplateImporter.check_disease_entries(ppkt_list)
         builder = HpoaTableBuilder(phenopacket_list=ppkt_list, created_by=self._created_by)
-        if moi == "Autosomal dominant":
-            builder.autosomal_dominant(pmid)
-        elif moi == "Autosomal recessive":
-            builder.autosomal_recessive(pmid)
-        elif moi == "X-linked inheritance":
-            builder.x_linked(pmid)
-        elif moi == "X-linked recessive inheritance":
-            builder.x_linked_recessive(pmid)
-        elif moi == "X-linked dominant inheritance":
-            builder.x_linked_dominant(pmid)
-        else:
-            raise ValueError(f"Did not recognize mode of inheritance {moi}")
+        builder.add_moi(mode_of_inheritance=mode_of_inheritance, pmid=pmid)
         hpoa_creator = builder.build()
         hpoa_creator.write_data_frame()
         return hpoa_creator.get_dataframe()

src/pyphetools/creation/mode_of_inheritance.py

@@ -0,0 +1,31 @@
+from enum import Enum
+from .hp_term import HpTerm
+
+class Moi(Enum):
+    AD="Autosomal dominant inheritance"
+    AR="Autosomal recessive inheritance"
+    XLI="X-linked inheritance"
+    XLR="X-linked recessive inheritance"
+    XLD="X-linked dominant inheritance"
+    MITO="Mitochondrial inheritance"
+    YLI="Y-linked inheritance"
+
+
+    def to_HPO(self):
+        if self == Moi.AD:
+            return HpTerm(hpo_id="HP:0000006", label="Autosomal dominant inheritance")
+        elif self == Moi.AR:
+            return HpTerm(hpo_id="HP:0000007", label="Autosomal recessive inheritance")
+        elif self == Moi.XLI:
+            return HpTerm(hpo_id="HP:0001417", label="X-linked inheritance")
+        elif self == Moi.XLR:
+            return HpTerm(hpo_id="HP:0001419", label="X-linked recessive inheritance")
+        elif self == Moi.XLD:
+            return HpTerm(hpo_id="HP:0001423", label="X-linked dominant inheritance")
+        elif self == Moi.MITO:
+            return HpTerm(hpo_id="HP:0001427", label="Mitochondrial inheritance")
+        elif self == Moi.YLI:
+            return HpTerm(hpo_id="HP:0001450", label="Y-linked inheritance")
+
+        else:
+            raise ValueError(f"Unrecognized Moi enum (should never happen)")

src/pyphetools/visualization/hpoa_table_creator.py

@@ -11,6 +11,7 @@
 from ..creation.hp_term import HpTerm
 from ..creation.individual import Individual
 from ..creation.metadata import MetaData
+from ..creation.mode_of_inheritance import Moi
 from .counted_hpo_term import CountedHpoTerm, CohortTermCounter
 from .onset_calculator import OnsetCalculator
 
@@ -347,6 +348,13 @@ def filter_diseases(disease_id, ppkt_list):
                     break
         print(f"[INFO] Extracted {(len(target_list))} from {(len(ppkt_list))} phenopackets with {disease_id}\n")
         return target_list
+
+    def add_moi(self, mode_of_inheritance:Moi, pmid:str):
+        """
+        Use this method to add mode of inheritance (MOI) data from a publication with the indicated pmid
+        """
+        self._moi_d[pmid].append(mode_of_inheritance)
+
 
     def autosomal_recessive(self, pmid):
         moi_term = HpTerm(hpo_id="HP:0000007", label="Autosomal recessive inheritance")

test/test_age_isoformater.py

@@ -1,66 +1,54 @@
-import unittest
+import pytest
 
 from pyphetools.creation import AgeIsoFormater
 
 
+class TestAgeIsoFormater:
+
+    @pytest.mark.parametrize(
+        'year, month, day, iso',
+        [
+            ( 2, 3,  5, "P2Y3M5D"),
+            ( 29, 5,  25, "P29Y5M25D"),
+            ( 99,1,24,"P99Y1M24D"),
+        ]
+    )
+    def test_ymd(
+        self,
+        year: int, 
+        month: int, 
+        day: int,
+        iso:str,
+    ):
+        iso_age = AgeIsoFormater.to_string(y=year, m=month, d=day)
+        assert iso == iso_age
+
+    @pytest.mark.parametrize(
+        'month, iso',
+        [
+            ( 5, "P5M"),
+            ( 0.5,"P15D"),
+            (0.8, "P24D"),
+            (11, "P11M"),
+            (12, "P1Y"),
+            (16, "P1Y4M"),
+            ("n.a.", "NOT_PROVIDED"),
+            (None, "NOT_PROVIDED"),
+            (float("nan"), "NOT_PROVIDED"),
+            (0, "P0D")
+        ]
+    )
+    def test_numerical_month(
+        self,
+        month: float, 
+        iso: str
+    ):
+        iso_age = AgeIsoFormater.from_numerical_month(month=month)
+        assert iso == iso_age
+
+
 
-class TestAgeIsoFormater(unittest.TestCase):
 
-    def test_basic1(self):
-        iso_age = AgeIsoFormater.to_string(y=2, m=3, d=5)
-        self.assertEqual("P2Y3M5D", iso_age)
-
-    def test_basic2(self):
-        """
-        test that 13 months are normalized to 1 year 1 month
-        """
-        iso_age = AgeIsoFormater.to_string(y=42, m=13, d=5)
-        self.assertEqual("P43Y1M5D", iso_age)
-
-    def test_5m(self):
-        iso_age = AgeIsoFormater.from_numerical_month(5)
-        self.assertEqual("P5M", iso_age)
-
-    def test_15d(self):
-        iso_age = AgeIsoFormater.from_numerical_month(0.5)
-        self.assertEqual("P15D", iso_age)
-
-    def test_24d(self):
-        iso_age = AgeIsoFormater.from_numerical_month(0.8)
-        self.assertEqual("P24D", iso_age)
-
-    def test_12m(self):
-        iso_age = AgeIsoFormater.from_numerical_month(12)
-        self.assertEqual("P1Y", iso_age)
-
-    def test_16m(self):
-        iso_age = AgeIsoFormater.from_numerical_month(16)
-        self.assertEqual("P1Y4M", iso_age)
-
-    def test_na(self):
-        """
-        Test we return NOT_PROVIDED (from the Contants class) if we cannot parse the cell contents
-        """
-        iso_age = AgeIsoFormater.from_numerical_month("n.a.")
-        self.assertEqual("NOT_PROVIDED", iso_age)
-
-    def test_none(self):
-        """
-        Test we return NOT_PROVIDED (from the Contants class) if we cannot parse the cell contents
-        """
-        iso_age = AgeIsoFormater.from_numerical_month(None)
-        self.assertEqual("NOT_PROVIDED", iso_age)
-
-    def test_nan(self):
-        """
-        Test we return NOT_PROVIDED (from the Contants class) if we cannot parse the cell contents
-        """
-        iso_age = AgeIsoFormater.from_numerical_month(float("nan"))
-        self.assertEqual("NOT_PROVIDED", iso_age)
-
-    def test_newborn(self):
-        iso_age = AgeIsoFormater.from_numerical_month(0)
-        self.assertEqual("P0D", iso_age)
 
 
 

test/test_moi.py

@@ -0,0 +1,59 @@
+import pytest
+
+from pyphetools.creation import Moi
+
+
+class TestMoi:
+
+    @pytest.mark.parametrize(
+        'moi, hpterm_id, hpterm_label',
+        [
+            (
+                    Moi.AD,
+                    'HP:0000006', 
+                    'Autosomal dominant inheritance',
+            ),
+            (
+                    Moi.AR,
+                    'HP:0000007',
+                    'Autosomal recessive inheritance',
+            ),
+            (
+                Moi.XLI,
+                'HP:0001417',
+                'X-linked inheritance'
+            ),
+            (
+                Moi.XLR,
+                'HP:0001419',
+                'X-linked recessive inheritance'
+            ),
+            (
+                Moi.XLD,
+                'HP:0001423',
+                'X-linked dominant inheritance'
+            ),
+            (
+                Moi.MITO,
+                'HP:0001427',
+                'Mitochondrial inheritance'
+            ),
+            (
+                Moi.YLI,
+                'HP:0001450',
+                'Y-linked inheritance'
+            )
+
+        ]
+    )
+    def test_moi(
+        self,
+        moi: Moi, 
+        hpterm_id: str, 
+        hpterm_label: str,
+    ):
+        hpterm = moi.to_HPO()
+
+        assert hpterm_id == hpterm.id
+        assert hpterm_label == hpterm.label
+