[Bioperl-l] Requesting your issues withModule:Bio::Tools::Run::RemoteBlast

[Chris Fields]

The only real change to RemoteBlast.pm made was to the save_output method;
it wasn't saving XML output because the regex used to check the tempfile
output:

	while(my $l = <TMP>) {
		next if ($l =~ /<pre>/);
		if( $l =~ /^(?:[T]?BLAST[NPX])\s*.+$/i ||
			 $l =~/^RPS-BLAST\s*.+$/i ) {
			$seentop=1;
		}
		next if !$seentop;
		if( $seentop ) {
			print SAVEOUT $l;
		}
	}

didn't check for XML.  I just added a check for XML that is the same as the
XML format check in the retrieve_blast method:

	while(my $l = <TMP>) {
		next if ($l =~ /<pre>/);
		if( $l =~ /^(?:[T]?BLAST[NPX])\s*.+$/i ||  # NCBI BLAST
			$l =~/^RPS-BLAST\s*.+$/i || # RPS BLAST
                  $1 =~/<\?xml version=/) { # NCBI BLAST XML output
			$seentop=1;
		}
		next if !$seentop;
		if( $seentop ) {
			print SAVEOUT $l;
		}
	}

There is probably a better way to do this, but it works for now.  All other
fixes were made to SearchIO::blast.  That module is where most of the work
is done and which 'broke' recently from the BLAST version change at NCBI.

The only things I can think of at the moment are things that Jason
mentioned, switching to XML as the default (I agree with) and possibly
incorporating the netblast client (blastcl3).  It might be possible to
branch off a similar module specifically geared towards the blastcl3 client,
maybe acting as a wrapper to parse the returned data using SearchIO, but I
don't necessarily think it would be best to include in RemoteBlast. 

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Roger Hall
> Sent: Friday, January 27, 2006 2:35 PM
> To: Bioperl-L
> Subject: [Bioperl-l] Requesting your issues
> withModule:Bio::Tools::Run::RemoteBlast
> 
> All,
> 
> 
> 
> I have a fun little application written around this module to track new
> hits
> for my favorite sequences, but it stopped working some time ago, so I have
> finally adopted this orphaned module.
> 
> 
> 
> I have received very specific suggestions from Jason and Chris for
> implementation, and plan to follow them in order to at least bring this
> module into the wonderful world of XML. I would appreciate it if you would
> send any additional features (and any known issues) my way.
> 
> 
> 
> Thanks!
> 
> 
> 
> Roger Hall
> 
> Technical Director
> 
> MidSouth Bioinformatics Center
> 
> University of Arkansas at Little Rock
> 
> (501) 569-8074
> 
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