#!/usr/bin/perl
# Demonstrates the use of a SearchIO Blast parser and a SearchWriterI object
# for producing tab-delimited output of hit data from a Blast report
# input stream.
#
# Each row in the output represents data for a single hit.
# For hits containing multiple HSPs, the output information represents a
# summary across all HSPs.
#
# 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 "hitwriter.out"
# containing tab-delimited data on a per-hit 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 HitTableWriter. This writer
# provides the same functionality as the original Bio::Tools::Blast::table()
# function (i.e., a tab-delimited summary of each hit per row).
# HitTableWriter, 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::HitTableWriter.
#
# 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::HitTableWriter;
# 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
num_hsps
expect
frac_aligned_query
frac_identical_query
length_aln_query
gaps_total
strand_query
strand_hit
);
# The following columns require HSP alignment data:
# num_hsps
# 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 file
# called "hitwriter.out"
# TODO: write hitless reports to STDERR and note if filtered.
my $in = Bio::SearchIO->new( -format => 'blast',
-fh => \*ARGV,
-signif => 0.1,
# -verbose=> 2
);
my $writer = Bio::SearchIO::Writer::HitTableWriter->new( -columns => \@columns
);
my $out = Bio::SearchIO->new( -format => 'blast',
-writer => $writer,
-file => ">hitwriter.out" );
# Need to keep a separate count of reports with hits
# to know when to include labels. The first report may be hitless,
# so we can't use $in->result_count
my $hit_count = 0;
while ( my $blast = $in->next_result() ) {
printf STDERR "\nReport %d: $blast\n", $in->result_count;
printf STDERR "query=%s, length=%d\n", $blast->query_name, $blast->query_length;
if( $blast->hits ) {
print STDERR "# hits= ", $blast->num_hits, "\n";
$hit_count++;
my @hits= $blast->hits;
print STDERR "frac_aligned_query= ", $hits[0]->frac_aligned_query, "\n";
$out->write_result($blast, $hit_count==1 );
}
else {
print STDERR "Hitless Blast Report ";
print STDERR ($blast->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;