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#!/usr/bin/perl
# Demonstrates the use of a SearchIO Blast parser and a SearchWriterI object
# for producing HTML Blast output from a Blast report input stream.
#
# Usage:
# STDIN: none; supply filename of BLAST report on command-line
# STDOUT: none; generates an output file "searchio.html"
# containing HTML-formatted Blast Report
# STDERR: Any errors that occurred.
#
# For more documentation about the writer, including
# a complete list of columns, see the docs for
# Bio::SearchIO::Writer::HTMLResultWriter.
#
# For more documentation about working with Blast result objects,
# see docs for these modules:
# Bio::Search::Result::BlastResult
# Bio::Search::Iteration::IterationI
# Bio::Search::Hit::BlastHit
# Bio::Search::HSP::BlastHSP
#
# For more documentation about the Blast parser, see docs for
# Bio::SearchIO
#
# Author: Steve Chervitz <sac@bioperl.org>
use strict;
use lib '../../';
use Bio::SearchIO;
use Bio::SearchIO::Writer::HTMLResultWriter;
my $outfile = "searchio.html";
my $file = shift or die "Usage: $0 <BLAST-report-file>\n HTML output is saved to $outfile\n";
my $in = Bio::SearchIO->new( -format => 'blast',
-file => $file, #comment this out to read STDIN
#-fh => \*ARGV, #uncomment this to read from STDIN
-verbose => 0 );
my $writer = new Bio::SearchIO::Writer::HTMLResultWriter();
my $out = new Bio::SearchIO(-writer => $writer,
-file => ">$outfile");
while ( my $result = $in->next_result() ) {
eval {
# printf STDERR "Report %d: $result\n", $in->result_count;
$out->write_result($result, 1);
};
if($@) {
warn "Warning: Blast parsing or writing exception caught for $result:\n$@\n";
}
}
printf STDERR "\n%d Blast report(s) processed.\n", $in->result_count;
printf STDERR "Output sent to file: %s\n", $out->file if $out->file;