[Bioperl-l] Re: Running BLAST locally

[Simon Chan]

Hi All,

*** Jason, thanks.  Your sugggestion worked!

So here's the code I've got:

my $factory = Bio::Tools::Run::StandAloneBlast->new ( database => 'refseq', program => 'blastn');

my $seq_in = Bio::SeqIO->new ( -file => 'inputfilename', -format => 'fasta');

my $seq = $seq_in->next_seq();

my $blast_report = $factory->blastall($seq); 

So now, I want to parse it.  I'm using BPlite.pm.  From the docs, this is how we use BPlite:

my $report = Bio::Tools::BPlite->new (-fh => \*STDIN);

So $blast_report contains the BLAST output in object form.  How would you pass $blast_report into BPlite?  I've tried outputting
$blast_report into a file using SeqIO and then inputting it into BPlite -file => "filename" (I know, that's a pretty odd way
of doing it ;-) and I've also tried using a filehandle to read in value like so:

open (INPUT, "<filename");
my $report = Bio::Tools::BPlite->new (-fh => \*INPUT);

So how would the non-rookie bio-perl users pass $blast_report into BPlite? :-)  The Pasteur tutorial is very good at showing rookies how to use modules, however, it doesn't spend too much time explaining  them.

Once again, many thanks, All.

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