[Bioperl-l] [Bioperl-guts-l] Notification: incoming/1215 (fwd)

[Jason Stajich]

t01051ki@sfc.keio.ac.jp

note that you can replace your
system("setenv BLASTDIR XXX");
calls which are shell and system dependent with
$ENV{'BLASTDIR'} = XXX;


You need to pass in Bio::Seq objects OR a filename to a fasta file when
you call blastall( );

So either build a Bio::Seq object --
blastall(new Bio::Seq(-seq =>$output[$count], -id => "Seq $count") );

or make your datafile look like a fasta file and pass in the name of the
file to blastall.



-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

---------- Forwarded message ----------
Date: Wed, 19 Jun 2002 00:55:38 -0400
From: bioperl-bugs@bioperl.org
To: bioperl-guts-l@bioperl.org
Subject: [Bioperl-guts-l] Notification: incoming/1215

JitterBug notification

new message incoming/1215

Message summary for PR#1215
	From: "Kyota Ishii" <t01051ki@sfc.keio.ac.jp>
	Subject: About  StandAloneBlast.pm
	Date: Wed, 19 Jun 2002 15:02:12  0900
	0 replies 	0 followups

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From: "Kyota Ishii" <t01051ki@sfc.keio.ac.jp>
To: <bioperl-bugs@bio.perl.org>
Cc: <bioperl-guts-l@bioperl.org>
Subject: About  StandAloneBlast.pm
Date: Wed, 19 Jun 2002 15:02:12 +0900
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I'm Japanese College students.
Sorry that I have poor English.

Now,I'm developing genome mapping tool.
>From Clustering result,adopt the longest gene.
And made list file about longest gene's name.

Then I 'm going to use StandAloneBlast.pm with for loop.
If array which put longest gene's name use in this module,

 MSG:  S3491
 (0) not Bio::Seq object or array of Bio::Seq objects or file name!
STACK Bio::Tools::Run::StandAloneBlast::blastall
/usr/lib/perl5/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm:452
STACK toplevel ./k_d_semifinal.pl:55

error happened.

I want to teach the reason which this program has bags.
----------------------------------------------------------------------------
-------------------------------------------
(My progarm used StandAloneBlast.pm)

#!/usr/bin/perl

use Bio::Tools::Run::StandAloneBlast;

system("setenv BLASTDIR /pub/software/blast");
system("setenv BLASTDATADIR /home/t01051ki/bioperl-1.0");

BEGIN{
    $ENV{BLASTDIR} = '/pub/software/blast';
    $ENV{BLASTDATADIR} = '/home/t01051ki/bioperl-1.0';
}

open(FILE,"gapsample");
$i=0;
while(<FILE>){

    if($_=~ /^[a-zA-Z0-9]/){
        $sentence1=$_;
        @bunkatu= split(/,/,$sentence1);
        ## print $bunkatu[0];
        @output[$i]=$bunkatu[0];
        $i ++;
    }
}

##foreach $item(@output){
##    print "$item\n";
##}
close FILE;

for($count=0;$count<$i;$count++){
    @params = ('program' => 'blastn','database' => 'H1_masked.fa','outfile'
=> 'blast'.$count.'out', '_READMETHOD' => 'Blast');
    $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
    $expectvalue=1.2;
    $factory->e($expectvalue);
##  Blast a sequence against a database:

    $blast_report = $factory->blastall($output[$count]);
}
----------------------------------------------------------------------------
-----------------------------------------
Keio College School in Japan
Kyota Ishii





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