bugfix: hh_reader alignments were not joined; hhmakemodel.py serious …

…bugs fixed by Hongbo Zhu
soedinglab · Jul 14, 2017 · d1b4893 · d1b4893
1 parent f74f336
commit d1b4893
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Showing 2 changed files with 209 additions and 60 deletions.
diff --git a/scripts/hh_reader.py b/scripts/hh_reader.py
@@ -16,8 +16,8 @@
 
 hhr_alignment = namedtuple('hhr_alignment', ['query_id', 'query_length', 'query_neff',
                                              'template_id', 'template_length', 'template_info',
-                                             'template_neff', 'query_ali', 'template_ali', 
-                                             'start', 'end', 'probability', 'evalue', 'score', 
+                                             'template_neff', 'query_ali', 'template_ali',
+                                             'start', 'end', 'probability', 'evalue', 'score',
                                              'aligned_cols', 'identity', 'similarity', 'sum_probs'])
 
 
@@ -169,7 +169,7 @@ def parse_result(lines):
     if(template_id is not None and query_start is not None):
         result = hhr_alignment(query_id, query_length, query_neff,
                                template_id, template_length, template_info, template_neff,
-                               query_seq, template_seq, (query_start, template_start),
+                               "".join(query_seq), "".join(template_seq), (query_start, template_start),
                                (query_end, template_end), probability, evalue, score,
                                aligned_cols, identity, similarity, sum_probs)
         results.append(result)