[Bioperl-pipeline] Dumper
shawnh@fugu-sg.org
shawnh@fugu-sg.org
Fri, 1 Nov 2002 09:38:33 +0800 (SGT)
Hi Folks,
I implemented a rudimentary flat file dumper for biopipe.
It actually is a standalone kinda thing whereby one can use it as
follows:
use Bio::Pipeline::Dumper;
use Bio::SearchIO;
my $dumper = Bio::Pipeline::Dumper->new(-module=>'blastscore',
-file=>">shawn.out",
-significance=>"<0.001",
-query_frac_identical=>">0.21");
my $searchio = Bio::SearchIO->new ('-format' => 'blast',
'-file' => "blast.report");
my @hit;
while (my $r = $searchio->next_result){
while(my $hit = $r->next_hit){
push @hit, $hit;
}
$dumper->dump(@hit);
Now I'm just dumping out blast scores in tab-delimited files:
Protein1 Protein2 1e-09
you can do filtering based on another of htings, significance,frac_conserved etc
The motivation for this is that for some use cases, thats all we
really want to feed it into the next analysis which takes in files
rather than a large operation to fetch objects from a db, write into file
and then run.
This module will be use as streamadaptor IOHandler.
I hope to add a gff dumper soon.
shawn
--
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************