Add new file

test/Test_representative_and_match/test_representative.py

+import pytest
+import pandas as pd
+import datatest as dt
+import representative as repr
+import numpy as np 
+import test_Functions as tFun
+
+
+def test_import_gtfSelection_to_df():
+    """
+    Test if gencode.vM31.annotation_intermediat_file.txt
+     is imported in the correct pandas df format
+        Args:
+            None
+
+        Returns:
+            Assert results 
+      
+        Raises:
+            None
+    """
+    path = tFun.find_path_intermediateFile()
+    df = repr.import_gtfSelection_to_df(path) 
+    datatype={'Gene': np.dtype('O'), 'Transcript': np.dtype('O'), 'Support_level': np.dtype('float64')}
+    assert tFun.column_number(df)==3, "number of columns is not equal to 3"
+    assert tFun.column_dType(df)==datatype, "at lease one column has the wrong datatype"
+    assert tFun.duplicated_rows(df).empty, "at lease one row are duplicated "
+    assert tFun.NA_value(df) == 0, "at lease one row contain NA values "
+    with pytest.raises(TypeError, match=r"Only str path is allowed"):
+        repr.import_gtfSelection_to_df(123)
+
+
+def test_representative_transcript_inDict(): 
+    """
+    Test if df generated by "import_gtfSelection_to_df()" output
+    a dict in the right format 
+        Args:
+            Pandas dataframe with [Gene, Transcript, Support_level]
+            as columns, validated with test_import_gtfSelection_to_df()
+
+        Returns:
+            Assert results 
+      
+        Raises:
+            None
+     """
+    path = tFun.find_path_intermediateFile()
+    df = repr.import_gtfSelection_to_df(path) 
+    dict_to_test = repr.representative_transcripts_inDict(df)
+    dict_expected = {'ENSMUSG00000024691': ['ENSMUST00000025595.5'], 
+    'ENSMUSG00000063683': ['ENSMUST00000044976.12', 'ENSMUST00000119960.2'], 
+    'ENSMUSG00000079415': ['ENSMUST00000112933.2']}
+    assert dict_to_test == dict_expected
+    with pytest.raises(TypeError, match=r"Only pandas DataFrame is allowed"):
+        repr.representative_transcripts_inDict(123)
+    with pytest.raises(TypeError, match=r"Only pandas DataFrame is allowed"):
+        repr.representative_transcripts_inDict("hello")
+    with pytest.raises(TypeError, match=r"Only pandas DataFrame is allowed"):
+        repr.representative_transcripts_inDict(["hello","world",123])
+    with pytest.raises(TypeError, match=r"Only pandas DataFrame is allowed"):
+        repr.representative_transcripts_inDict({"hello":"world", "bonjour":["le monde", 123]})
+
+def test_find_repr_by_SupportLevel():
+    """
+    Test if the correct dict is generated from gencode.vM31.annotation_intermediat_file.txt
+        Args:
+            None 
+
+        Returns:
+            Assert results 
+      
+        Raises:
+            None
+    """
+    path = tFun.find_path_intermediateFile()
+    dict_to_test = repr.find_repr_by_SupportLevel(path)
+    dict_expected = {'ENSMUSG00000024691': ['ENSMUST00000025595.5'], 
+    'ENSMUSG00000063683': ['ENSMUST00000044976.12', 'ENSMUST00000119960.2'], 
+    'ENSMUSG00000079415': ['ENSMUST00000112933.2']}
+    assert dict_to_test == dict_expected
+
+test_representative_transcript_inDict()
+test_find_repr_by_SupportLevel()
+test_import_gtfSelection_to_df()
+print("test_representative is done ! No error was found")