[Biopython-dev] [Biopython - Bug #3400] (New) Hmmer3-text parser crashes when parsing hmmscan --cut_tc files

[redmine at redmine.open-bio.org]

Issue #3400 has been reported by Kai Blin.

----------------------------------------
Bug #3400: Hmmer3-text parser crashes when parsing hmmscan --cut_tc files
https://redmine.open-bio.org/issues/3400

Author: Kai Blin
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


I'm currently struggling with a crash in the hmmer3-text parser when dealing with files generated by hmmscan --cut_tc.
I'm not quite sure what happens yet, but I have the feeling that some part of the hit parsing logic is reading into the next query without yielding a result.

The backtrace is
<pre>
Traceback (most recent call last):
  File "t.py", line 4, in <module>
    i = it.next()
  File "/data/uni/biopython/Bio/SearchIO/__init__.py", line 317, in parse
    yield qresult
  File "/usr/lib/python2.6/contextlib.py", line 34, in __exit__
    self.gen.throw(type, value, traceback)
  File "/data/uni/biopython/Bio/File.py", line 84, in as_handle
    yield fp
  File "/data/uni/biopython/Bio/SearchIO/__init__.py", line 316, in parse
    for qresult in generator:
  File "/data/uni/biopython/Bio/SearchIO/HmmerIO/hmmer3_text.py", line 47, in __iter__
    for qresult in self._parse_qresult():
  File "/data/uni/biopython/Bio/SearchIO/HmmerIO/hmmer3_text.py", line 133, in _parse_qresult
    hit_list = self._parse_hit(qid)
  File "/data/uni/biopython/Bio/SearchIO/HmmerIO/hmmer3_text.py", line 176, in _parse_hit
    hit_list = self._create_hits(hit_attr_list, qid)
  File "/data/uni/biopython/Bio/SearchIO/HmmerIO/hmmer3_text.py", line 239, in _create_hits
    hit_attr = hit_attrs.pop(0)
IndexError: pop from empty list
</pre>

Line numbers might be a bit off as I added debug output to understand what's happening already.


----------------------------------------
You have received this notification because this email was added to the New Issue Alert plugin


-- 
You have received this notification because you have either subscribed to it, or are involved in it.
To change your notification preferences, please click here and login: http://redmine.open-bio.org