[Bioperl-l] Bio::Tools::Run::StandAloneBlast can't find path to blastall

[Mark A. Jensen]

You've got blast+, so have a look at Bio::Tools::Run::StandAloneBlastPlus,
should solve it. MAJ
----- Original Message ----- 
From: "mindlessbrain" <jillianrowe91286 at gmail.com>
To: <Bioperl-l at lists.open-bio.org>
Sent: Monday, May 03, 2010 8:42 AM
Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlast can't find path to 
blastall


>
> Hey all,
>
> I'm trying to run some code for StandAloneBLast in Windows Vista:
>
> [code]
> #!/usr/bin/perl
>
> use Bio::DB::SwissProt;
> use Bio::Tools::Run::StandAloneBlast;
>
> BEGIN
> {
> $ENV{PATH}="D:/blast-2.2.23+/bin/:";
> }
>
> my $database = new Bio::DB::SwissProt;
> my $query = $database->get_Seq_by_id('TAUD_ECOLI');
>
> my $factory = Bio::Tools::Run::StandAloneBlast->new(
> 'program'  => 'blastp',
> 'database' => 'swissprot',
> _READMETHOD => "Blast"
> );
> my $blast_report = $factory->blastall($query);
> my $result = $blast_report->next_result;
> while( my $hit = $result->next_hit()) {
>    print "\thit name: ", $hit->name(),
>    " significance: ", $hit->significance(), "\n";
> }
> [/code]
>
> I installed BLAST from the NCBI website. I get this when I run dir on the
> bin:
>
> D:\blast-2.2.23+\bin>dir
> Volume in drive D has no label.
> Volume Serial Number is 224C-0190
>
> Directory of D:\blast-2.2.23+\bin
>
> 05/03/2010  03:02 PM    <DIR>          .
> 05/03/2010  03:02 PM    <DIR>          ..
> 03/08/2010  11:09 PM         2,789,376 blastdbcheck.exe
> 03/08/2010  11:09 PM         4,009,984 blastdbcmd.exe
> 03/08/2010  11:09 PM         1,810,432 blastdb_aliastool.exe
> 03/08/2010  11:09 PM         6,225,920 blastn.exe
> 03/08/2010  11:09 PM         6,221,824 blastp.exe
> 03/08/2010  11:09 PM         6,213,632 blastx.exe
> 03/08/2010  11:09 PM         5,316,608 blast_formatter.exe
> 03/08/2010  11:09 PM         3,215,360 convert2blastmask.exe
> 03/08/2010  11:09 PM         3,211,264 dustmasker.exe
> 03/08/2010  11:09 PM            51,178 legacy_blast.pl
> 03/08/2010  11:09 PM         3,866,624 makeblastdb.exe
> 03/08/2010  11:09 PM         3,612,672 makembindex.exe
> 03/08/2010  11:09 PM         6,344,704 psiblast.exe
> 03/08/2010  11:09 PM         6,201,344 rpsblast.exe
> 03/08/2010  11:09 PM         6,205,440 rpstblastn.exe
> 03/08/2010  11:09 PM         3,608,576 segmasker.exe
> 03/08/2010  11:09 PM         6,320,128 tblastn.exe
> 03/08/2010  11:09 PM         6,209,536 tblastx.exe
> 03/08/2010  11:09 PM            10,010 update_blastdb.pl
> 03/08/2010  11:09 PM         3,530,752 windowmasker.exe
>              20 File(s)     84,975,364 bytes
>               2 Dir(s)  122,390,626,304 bytes free
>
> I have an ncbi.ini file in my windows directory that contains:
> [NCBI]
> DATA=D:\blast-2.2.23+\data
> [BLAST]
> BLASTDB=D:\blast-2.2.23+\db
>
> Here's what my environmental variables looks like:
>
> http://old.nabble.com/file/p28434717/environmental%2Bvariables.jpg
>
> Help would be very, very appreciated!
>
>
> -- 
> View this message in context: 
> http://old.nabble.com/Bio%3A%3ATools%3A%3ARun%3A%3AStandAloneBlast-can%27t-find-path-to-blastall-tp28434717p28434717.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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