[Bioperl-l] Output of a BLAST parse to text file

[Frank Schwach]

Hi Tiago,

In the terminal where you run your script (let's say it's called
my_blast_parse.pl), you can run it like so:

my_blast_parse.pl [PARAMETERS] > my_outfile.txt

The ">" will redirect the output to a file calles my_outfile.txt.
To make the output tab-delimited, you will want to play with the print
statement in the script. try this for a start (the "\t" inserts tabs):

print
$result->query_name."\t".$hit->name."\t".$hsp->length('total')."\t".
$hsp->percent_identity, "\n";


Good luck!

Frank



On Sun, 2011-04-10 at 15:56 -0700, T.Hori wrote:
> Hi Guys,
> 
> I am really new to BioPerl, so this may be a stuoid question. Let's
> say I use the example from the BioPerl.org:
> 
> use strict;
> use Bio::SearchIO;
> my $in = new Bio::SearchIO(-format => 'blast',
>                            -file   => 'report.bls');
> while( my $result = $in->next_result ) {
>   ## $result is a Bio::Search::Result::ResultI compliant object
>   while( my $hit = $result->next_hit ) {
>     ## $hit is a Bio::Search::Hit::HitI compliant object
>     while( my $hsp = $hit->next_hsp ) {
>       ## $hsp is a Bio::Search::HSP::HSPI compliant object
>       if( $hsp->length('total') > 50 ) {
>         if ( $hsp->percent_identity >= 75 ) {
>           print "Query=",   $result->query_name,
>             " Hit=",        $hit->name,
>             " Length=",     $hsp->length('total'),
>             " Percent_id=", $hsp->percent_identity, "\n";
>         }
>       }
>     }
>   }
> }
> 
> That gives me several hits as results on the standard output. I am
> starting to learn BioPerl for what I think is a dauting task. I have a
> colletion of 20K ESTs and I have to find the best Human hit for
> everyone of those sequences. So I am starting by learning how to parse
> BLAST results. I was wondering how I would go about having the output
> of the parse go to tab-delimeted text file instead of the standard
> output.
> 
> Any help would be greatly appreciated.
> 
> Thanks,
> 
> Tiago
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