[Bioperl-l] Blast parsing exception

Marc Logghe MarcL@DEVGEN.com
Mon, 22 Oct 2001 09:16:34 +0200

Thanks for the reply Hilmar,
The version is:
$Id: Blast.pm,v 1.19 2001/05/16 14:57:44 heikki Exp $
It behaves the same on al Linux and WindowsNT box (same version of Bioperl
installed 0.9.0).
In my previous post I presented a fix. Forget about it. I must have been
dreaming. It is more complicated than that.
In the _get_parse_blast_func subroutine 3 possible chunk types are
mentioned. I think the problem is there are more of them 
##   1. Header with description section,
##   2. An alignment section for a single hit, or
##   3. The final alignment section plus the footer section.
In my case eg, a chunk contained 'The final alignment section plus the
footer section' of report x plus complete report x+1 (no hits) plus complete
report x+2 (no hits neither) + header/description section of report x+3. And
what if a multiple report stream starts with a 'no hits' report ?
It is also not clear to me yet whether a 'no hit' report is parsed or not,
eg is the _name property of the query set or not. Anyhow, when I find the
time I'll try to find this out today.
To answer the question about the report type: Blastp output produced by NCBI
Blast 2.2.1 (see snippet one of my previous postings)
> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp@gmx.net]
> Sent: Monday, October 22, 2001 8:38 AM
> To: Marc Logghe
> Cc: 'bioperl-l@bioperl.org'
> Subject: Re: [Bioperl-l] Blast parsing exception
> Marc Logghe wrote:
> > 
> > Found the bug. When I commented out completely this code 
> snippet from
> > Bio::Tools::Blast
> > 
> >               # Incyte_Fix:   Nasty Invisible Bug.
> Which version are you using, and which report type? I remember I
> fixed this myself couple of months ago already, as it was reported
> several times. I thought I was fine meanwhile. -hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                              email: hilmarl@yahoo.com
> San Diego, Ca. 92130                     phone: +1 858 812 1757
> -----------------------------------------------------------------