本地blast bioperl

freesiaSS

我想用bioperl 本地blast,
配置了~/.bashrc   BLASTDB=/usr/local/Cellar/blast/2.4.0/db
设置了环境变量  $ export PATH=$PATH:/usr/local/Cellar/blast/2.4.0/bin
                      $ echo $PATH
/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/go/bin:/usr/local/ncbi/blast/bin:/usr/local/Cellar/blast/2.4.0/bin

可是还是出现了警告
--------------------- WARNING ---------------------
MSG: cannot find path to blastall
---------------------------------------------------


代码如下：
use Bio::SearchIO;
use Bio::Tools::Run::StandAloneBlast;


my $file = shift;
my $outfile = $file."_blast.out";
my $blast_obj = Bio::Tools::Run::StandAloneBlast->new(-program => '/usr/local/Cellar/blast/2.4.0/bin/blastn', -database => '/usr/local/Cellar/blast/2.4.0/db/plant.mt.ss', -expect => 0.01, -outfile => "$outfile", );
my $blast_report = $blast_obj->blastall('/Users/sshu/desktop/Query.fasta');

我安装了blast+/blast,两个都不能被bioperl成功召唤
我不知道哪里出错了，请问谁可以解决这个问题啊
SOS

SilenceGene

提示信息是无法找到blastall程序，这个blastall是blast里面带的程序，你不应该指定到blastn程序上，而是应该指定到blast/bin/blastall上