parse signalp v6 #650

funannotate/library.py

@@ -5654,6 +5654,8 @@ def parseSignalP(sigP, secretome_annot):
             if line.startswith('#'):
                 if line.startswith('# SignalP-5'):
                     version = 5
+                elif line.startswith('# SignalP-6'):
+                    version = 6
                 continue
             if version < 5:
                 col = line.split(' ')  # not tab delimited
@@ -5662,7 +5664,7 @@ def parseSignalP(sigP, secretome_annot):
                     ID = col[0]
                     end = int(col[2]) - 1
                     sigpDict[ID] = [end, '', '']
-            else:  # version 5 has different format and tab delimited hooray!
+            elif version == 5:  # version 5 has different format and tab delimited hooray!
                 if '\t' in line:
                     cols = line.split('\t')
                     if cols[1] != 'OTHER':  # then signal peptide
@@ -5672,6 +5674,15 @@ def parseSignalP(sigP, secretome_annot):
                         prob = components[-1]
                         aa = components[3].replace('.', '')
                         sigpDict[ID] = [pos, aa, prob]
+            else:
+                if '\t' in line:
+                    cols = line.split('\t')
+                    if cols[1] != 'NO_SP':  # then signal peptide
+                        ID, prediction, score1, score2, position = cols[:5]
+                        components = position.split()
+                        pos = components[2].split('-')[0]
+                        prob = components[-1]
+                        sigpDict[ID] = [pos, '', prob]
 
     with open(secretome_annot, 'w') as secout:
         for k, v in natsorted(list(sigpDict.items())):