#!/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);