[Bioperl-l] Is it possible to parse BLAST output using IO:String?

Ryan Golhar golharam at umdnj.edu
Mon Oct 30 20:11:51 UTC 2006

I'm trying to parse some blast output w/o actually creating the output
file.  Instead, I'm capturing the output in a variable and would like to
use IO::String to represent the file:

	$_ = `megablast -d somedatabase -i somesequence -D 2`;
	my $blast_file = new IO::String($_);
	my $searchio = new Bio::SearchIO(-format => 'blast', -fh =>
	my $results = $searchio->next_result;
	my $hit = $results->next_hit;
	if (! defined($hit)) {
		warn "No BLAST hit for $accession on chr $chr for

Now, when Bio::SearchIO tries to read the output line by line, instead
it reads the entire output as 1 line.

If I provide the output in a file and use:

	my $searchio = new Bio::SearchIO(-format => 'blast', -file =>

This works...so is it possible to use IO::String to provide
Bio::SearchIO with BLAST output?  


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