fixed a bug due to long indels during hmmsearch output processing

scripts/parseHMMER.py

@@ -63,10 +63,12 @@ def parseHMMER(fh,hmmDict):
             # process each domain hit (i.e., hmm-seq alignment)
             while line and line.lstrip().startswith("== domain "):
                 tokens = line.split()
-                hit = hitTable[ int(tokens[2])-1 ]
+                hit_index = int(tokens[2])-1
+                hit = hitTable[hit_index]
                 hmm_cons = ""
                 seq_cons = ""
                 pp_cons  = ""
+                aln_to = 0
                 while True:
                     line = fh.readline()
                     tokens = line.split()
@@ -78,7 +80,8 @@ def parseHMMER(fh,hmmDict):
                         hit.match_str += match_line[ match_cons_i : match_cons_i+len(tokens[2]) ]
                         tokens = fh.readline().split()
                         seq_cons += tokens[2]
-                        aln_to = int(tokens[3])
+                        if tokens[3].isdigit():
+                            aln_to = int(tokens[3])
                         tokens = fh.readline().split()
                         pp_cons += tokens[0]
                         if aln_to == hit.ali_to: