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#!/usr/bin/perl
# Demonstrates the use of a SearchIO parser for processing
# the iterations within a PSI-BLAST report.
#
# Usage:
# STDIN: none; supply filename of PSI-BLAST report on command-line
# STDOUT: information parsed from the input data.
# STDERR: errors.
#
# For more documentation about working with Iteration objects,
# see docs for:
# Bio::Search::Iteration::IterationI
#
# Author: Steve Chervitz <sac@bioperl.org>
use strict;
use lib '../../';
use Bio::SearchIO;
my $file = shift or die "Usage: $0 <BLAST-report-file>\n";
my $in = new Bio::SearchIO(-format => 'blast',
-file => $file, #comment this out to read STDIN
#-fh => \*ARGV, #uncomment this to read STDIN
);
# Iterate over all results in the input stream
while (my $result = $in->next_result) {
printf "Result #%d: %s\n", $in->result_count, $result->to_string;
printf "Total Iterations: %d\n", $result->num_iterations();
# Iterate over all iterations and process old and new hits
# separately.
while( my $it = $result->next_iteration) {
printf "\nIteration %d\n", $it->number;
printf "Converged: %d\n", $it->converged;
# Print out the hits not found in previous iteration
printf "New hits: %d\n", $it->num_hits_new;
while( my $hit = $it->next_hit_new ) {
printf " %s, Expect=%g\n", $hit->name, $hit->expect;
}
# Print out the hits found in previous iteration
printf "Old hits: %d\n", $it->num_hits_old;
while( my $hit = $it->next_hit_old ) {
printf " %s, Expect=%g\n", $hit->name, $hit->expect;
}
}
printf "%s\n\n", '-' x 50;
}
printf "Total Reports processed: %d: %s\n", $in->result_count;
__END__
# NOTE: The following functionality is just proposed
# (does not yet exist but might, given sufficient hew and cry):
# Zero-in on the new hits found in last iteration.
# By default, iteration() returns the last one.
my $last_iteration = $result->iteration();
while( my $hit = $last_iteration->next_hit) {
# Do something with new hit...
}
# Get the first iteration
my $first_iteration = $result->iteration(1);