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

[Brad Chapman]

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):