Merge branch '30-genomics_ihc' into 'master'

Resolve "Update cancer gene"

Closes #30

See merge request !12

scripts/transform_germline_mutations.py

@@ -64,6 +64,19 @@ def convert_number(merged, significance):
     return merged
 
 
+def reformat_gene(merged):
+    '''Converts gene names to apporpriate string for database'''
+
+    merged['Gene'] = merged['Gene'].astype(str) + '(Sequencing)'
+
+    # If IHC then switch
+    pat = r"^IHC(?P<one>\w+)\((Sequencing\))"
+    repl = lambda m: m.group('one') + '(IHC)'
+
+    merged.Gene = merged.Gene.str.replace(pat, repl, regex=True)
+    return merged
+
+
 def calculate_shift(cancer_gene, date_shift):
     '''Shift Date for start date'''
 
@@ -117,8 +130,11 @@ def main():
     # Convert missing Number
     fix_number = convert_number(cancer_gene_reformat, significance_map)
 
+    # Convert gene names
+    fix_gene = reformat_gene(fix_number)
+
     # Calculate Date Shift
-    shifted_df = calculate_shift(fix_number, date_shift)
+    shifted_df = calculate_shift(fix_gene, date_shift)
 
     # Write out radiation table
     shifted_df.to_csv(cancer_gene_table, index=False)

scripts/transform_patients.py

@@ -109,7 +109,10 @@ def calculate_shift(merged):
     merged['BIRTH_DATE'] = pd.to_datetime(merged['BIRTH_DATE'])
     merged['DEATH_DATE'] = pd.to_datetime(merged['DEATH_DATE'])
     merged['Date of Last Contact-Date'] = pd.to_datetime(merged['Date of Last Contact-Date'])
-    merged['Date of Diagnosis'] = pd.to_datetime(merged['Date of Diagnosis'])
+    if 'Date of Diagnosis' in merged.columns:
+        merged['Date of Diagnosis'] = pd.to_datetime(merged['Date of Diagnosis'])
+    else:
+        merged['Date of Diagnosis'] = pd.NaT
 
 
     # Calculate date shift relative to 1800/01/01

tests/test_transform_germline.py

@@ -112,3 +112,11 @@ def test_check_convert_number_5(germline_5, significance_map):
     converted_germline = transform_germline_mutations.convert_number(transform_germline, significance_map)
     row_selection = converted_germline[converted_germline['Gene'] == 'SDHC'].index.item()
     assert converted_germline.loc[row_selection, 'Number'] == 'Pending'
+
+
+@pytest.mark.unit
+def test_check_reformat_gene(germline_5):
+    transform_germline = transform_germline_mutations.reformat_record(germline_5)
+    converted_germline = transform_germline_mutations.reformat_gene(transform_germline)
+    row_selection = converted_germline[converted_germline['Gene'].str.match(r'SDHC')==True].index.item()
+    assert converted_germline.loc[row_selection, 'Gene'] == 'SDHC(Sequencing)'