examples/searchio/psiblast_iterations.pl

   1 #!/usr/bin/perl
   2
   3 # Demonstrates the use of a SearchIO parser for processing
   4 # the iterations within a PSI-BLAST report.
   5 #
   6 # Usage:
   7 #   STDIN:  none; supply filename of PSI-BLAST report on command-line
   8 #   STDOUT: information parsed from the input data.
   9 #   STDERR: errors.
  10 #
  11 # For more documentation about working with Iteration objects,
  12 # see docs for:
  13 #   Bio::Search::Iteration::IterationI
  14 #
  15 # Author: Steve Chervitz <sac@bioperl.org>
  16
  17 use strict;
  18 use lib '../../';
  19
  20 use Bio::SearchIO;
  21
  22 my $file = shift or die "Usage: $0 <BLAST-report-file>\n";
  23 my $in = new Bio::SearchIO(-format => 'blast',
  24                            -file => $file, #comment this out to read STDIN
  25                            #-fh => \*ARGV,  #uncomment this to read STDIN
  26                           );
  27
  28 # Iterate over all results in the input stream
  29 while (my $result = $in->next_result) {
  30
  31     printf "Result #%d: %s\n", $in->result_count, $result->to_string;
  32     printf "Total Iterations: %d\n", $result->num_iterations();
  33
  34     # Iterate over all iterations and process old and new hits
  35     # separately.
  36
  37     while( my $it = $result->next_iteration) {
  38         printf "\nIteration %d\n", $it->number;
  39         printf "Converged: %d\n", $it->converged;
  40
  41         # Print out the hits not found in previous iteration
  42         printf "New hits: %d\n", $it->num_hits_new;
  43         while( my $hit = $it->next_hit_new ) {
  44             printf "  %s, Expect=%g\n", $hit->name, $hit->expect;
  45         }
  46
  47         # Print out the hits found in previous iteration
  48         printf "Old hits: %d\n", $it->num_hits_old;
  49         while( my $hit = $it->next_hit_old ) {
  50             printf "  %s, Expect=%g\n", $hit->name, $hit->expect;
  51         }
  52     }
  53     printf "%s\n\n", '-' x 50;
  54 }
  55
  56 printf "Total Reports processed: %d: %s\n", $in->result_count;
  57
  58 __END__
  59
  60 # NOTE: The following functionality is just proposed
  61 # (does not yet exist but might, given sufficient hew and cry):
  62
  63 # Zero-in on the new hits found in last iteration.
  64 # By default, iteration() returns the last one.
  65
  66 my $last_iteration = $result->iteration();
  67 while( my $hit = $last_iteration->next_hit) {
  68     # Do something with new hit...
  69 }
  70
  71 # Get the first iteration
  72
  73 my $first_iteration = $result->iteration(1);
  74