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#!/usr/bin/env perl
# Demonstrates the use of a SearchIO Blast parser and a SearchWriterI object
# for producing tab-delimited output of HSP data from a Blast report
# input stream.
#
# Each row in the output represents data for a single HSP.
#
# This parser represents a new and improved version of Bio::Tools::Blast.
#
# Usage:
# STDIN: stream containing one or more BLAST or PSI-BLAST reports.
# STDOUT: none, but generates an output file "hspwriter.out"
# containing tab-delimited data on a per-HSP basis.
# STDERR: Progress info and any errors.
#
# In this example, we create a SearchIO parser that screens out hits
# based on expect (or P) scores and a default HSPTableWriter. This writer
# provides the same functionality as the original Bio::Tools::Blast::table2()
# function (i.e., a tab-delimited summary of each hit per row).
# HSPTableWriter, however, is customizable so you can specify just the columns
# you want to have in the output table.
#
# For more documentation about the writer, including
# a complete list of columns, execute:
# perldoc Bio::SearchIO::Writer::HSPTableWriter.
#
# 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::HSPTableWriter;
# These are the columns that will be in the output table of BLAST results.
my @columns = qw(
query_name
query_length
hit_name
hit_length
rank
expect
frac_identical_query
length_aln_query
gaps_total
strand_query
strand_hit
);
print STDERR "\nUsing SearchIO->new()\n";
# Note that all parameters for the $in, $out, and $writer objects are optional.
# Default in = STDIN; Default out = STDOUT; Default writer = all columns
# In this example, we're reading from STDIN and writing to a STDOUT
my $in = Bio::SearchIO->new( -format => 'blast',
-fh => \*ARGV
);
my $writer = Bio::SearchIO::Writer::HSPTableWriter->new( -columns => \@columns );
my $out = Bio::SearchIO->new( -format => 'blast',
-writer => $writer,
-file => ">hspwriter.out" );
while ( my $result = $in->next_result() ) {
printf STDERR "\nReport %d: $result\n", $in->result_count;
if( $result->hits ) {
$out->write_result($result, ($in->result_count - 1 ? 0 : 1) );
}
else {
print STDERR "Hitless Blast Report: $result ";
print STDERR ($result->no_hits_found ? "\n" : "(filtered)\n");
}
## For a simple progress monitor, uncomment this line:
#print STDERR "."; print STDERR "\n" if $in->result_count % 50 == 0;
}
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;