Merge pull request #170 from oncokb/fix-missing-columns

Check whether level exists in the input file
oncokb · Apr 27, 2022 · 7f6913b · 7f6913b
2 parents 1458c17 + 13ad23c
commit 7f6913b
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/AnnotatorCore.py b/AnnotatorCore.py
@@ -976,8 +976,8 @@ def processclinicaldata(annotatedmutfiles, clinicalfile, outfile):
                     sampledrivers[sample].append(variant)
 
                 for l in levels:
-                    il = headers[l]
-                    if il < len(row) and row[il] != '':
+                    il = geIndexOfHeader(headers, [l])
+                    if 0 <= il < len(row) and row[il] != '':
                         if l not in samplelevels[sample]:
                             samplelevels[sample][l] = []
                             sampleleveltreatments[sample][l] = []
@@ -988,15 +988,15 @@ def processclinicaldata(annotatedmutfiles, clinicalfile, outfile):
                             sampleactionablecount[sample][variant] = True
 
                 for l in dxLevels:
-                    il = headers[l]
-                    if il < len(row) and row[il] != '':
+                    il = geIndexOfHeader(headers, [l])
+                    if 0 <= il < len(row) and row[il] != '':
                         if l not in samplelevels[sample]:
                             samplelevels[sample][l] = []
                         samplelevels[sample][l].append(row[il] + "(" + variant + ")")
 
                 for l in pxLevels:
-                    il = headers[l]
-                    if il < len(row) and row[il] != '':
+                    il = geIndexOfHeader(headers, [l])
+                    if 0 <= il < len(row) and row[il] != '':
                         if l not in samplelevels[sample]:
                             samplelevels[sample][l] = []
                         samplelevels[sample][l].append(row[il] + "(" + variant + ")")