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
  19 use Bio::SearchIO;
  20
  21 my $file = shift or die "Usage: $0 <BLAST-report-file>\n";
  22 my $in = new Bio::SearchIO(-format => 'blast',
  23                            -file => $file, #comment this out to read STDIN
  24                            #-fh => \*ARGV,  #uncomment this to read STDIN
  25                           );
  26
  27 # Iterate over all results in the input stream
  28 while (my $result = $in->next_result) {
  29
  30     printf "Result #%d: %s\n", $in->result_count, $result->to_string;
  31     printf "Total Iterations: %d\n", $result->num_iterations();
  32
  33     # Iterate over all iterations and process old and new hits
  34     # separately.
  35
  36     while( my $it = $result->next_iteration) {
  37         printf "\nIteration %d\n", $it->number;
  38         printf "Converged: %d\n", $it->converged;
  39
  40         # Print out the hits not found in previous iteration
  41         printf "New hits: %d\n", $it->num_hits_new;
  42         while( my $hit = $it->next_hit_new ) {
  43             printf "  %s, Expect=%g\n", $hit->name, $hit->expect;
  44         }
  45
  46         # Print out the hits found in previous iteration
  47         printf "Old hits: %d\n", $it->num_hits_old;
  48         while( my $hit = $it->next_hit_old ) {
  49             printf "  %s, Expect=%g\n", $hit->name, $hit->expect;
  50         }
  51     }
  52     printf "%s\n\n", '-' x 50;
  53 }
  54
  55 printf "Total Reports processed: %d: %s\n", $in->result_count;
  56
  57 __END__
  58
  59 # NOTE: The following functionality is just proposed
  60 # (does not yet exist but might, given sufficient hew and cry):
  61
  62 # Zero-in on the new hits found in last iteration.
  63 # By default, iteration() returns the last one.
  64
  65 my $last_iteration = $result->iteration();
  66 while( my $hit = $last_iteration->next_hit) {
  67     # Do something with new hit...
  68 }
  69
  70 # Get the first iteration
  71
  72 my $first_iteration = $result->iteration(1);
  73