[Biopython-dev] Parser problem with blastpgp v. 2.0.13?

[Jeffrey Chang]

Hi Iddo,

Yes, there's definitely a bug here.  The problem is that the master-slave
alignment code wasn't built with PSI-BLAST in mind.  When it encounters a
master-slave alignment, it keeps on parsing until it finds the database
section.  Unfortunately, this breaks with PSI-BLAST, since it generates
many alignments in a single run.

The fix, as Brad noted, is to allow the masterslave code to recognize
psi-blast output.  This has been checked in and will go into the next
developmental release.

Thanks for the report and the fix!

Jeff


On 1 Oct 2000, Brad Chapman wrote:

> Iddo wrote:
> >  I already submitted a bug report (#16). Basically, i cannot seem to
> >  work the NCBIStandalone parser with the output I get. I did run it on
> >  similar btXXX files, and that seemed to go well.
> >
> >  I am using blastpgp V 2.0.13
> 
> Hmmm... I took a quick look at this, and I think this is the problem. It
> looks from the comments that Jeff has only tested this with v 2.0.10 and
> v 2.0.11 so it looks like the output has changed somewhat (of course!).
> 
> I think the problem is that _scan_masterslave_alignment isn't figuring
> out that it should stop reading alignments, so it is trying to convert
> '....' into an integer, which obviously didn't work so hot.
> 
> The new break between between rounds is a Searching.... line, instead of
> the Database line that _scan_masterslave_alignment is looking for, so if
> you add a check to break on finding Searching..., then the parse seems to
> complete okay.
> 
> I was playing with this to look at the results, and it also looks like
> the record isn't giving up the data from the multiple alignments, so I
> also had a quick patch to fix this. 
> 
> Here are the patches, against CVS, that seem to make things look okay for
> me. Jeff is the master of Blast, so it is up to him to approve these (or
> let me know where I went wrong :-). Hope this helps.
> 
> Brad
> 
> *** NCBIStandalone.py.orig	Sun Oct  1 18:36:01 2000
> --- NCBIStandalone.py	Sun Oct  1 19:47:27 2000
> ***************
> *** 329,335 ****
> 	  consumer.start_alignment()
> 	  while 1:
> 	      line = safe_readline(uhandle)
> !	      if line[:10] == '  Database':
> 		  uhandle.saveline(line)
> 		  break
> 	      elif is_blank_line(line):
> --- 329,340 ----
> 	  consumer.start_alignment()
> 	  while 1:
> 	      line = safe_readline(uhandle)
> !	      # PSIBlast 2.0.13 appears to have a Searching... line after
> !	      # rounds instead of a Database line
> !	      if line[:9] == 'Searching':
> !		  uhandle.saveline(line)
> !		  break
> !	      elif line[:10] == '  Database':
> 		  uhandle.saveline(line)
> 		  break
> 	      elif is_blank_line(line):
> ***************
> *** 1178,1184 ****
> 	  _AlignmentConsumer.end_alignment(self)
> 	  if self._alignment is not None:
> 	      self._round.alignments.append(self._alignment)
> !	  elif self._multiple_alignment is not None:
> 	      self._round.multiple_alignment = self._multiple_alignment
>   
>       def end_hsp(self):
> --- 1183,1189 ----
> 	  _AlignmentConsumer.end_alignment(self)
> 	  if self._alignment is not None:
> 	      self._round.alignments.append(self._alignment)
> !	  if self._multiple_alignment is not None:
> 	      self._round.multiple_alignment = self._multiple_alignment
>   
>       def end_hsp(self):
> 
> 
> 
> 
> 
> 
> 
> 
> 
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