examples/searchio/rawwriter.pl

   1 #!/usr/bin/env perl
   2
   3 # Demonstrates the use of a SearchIO Blast parser for producing
   4 # output of raw HSP data from a Blast report input stream.
   5 #
   6 # Shows how to print out raw BLAST alignment data for each HSP.
   7 #
   8 # Usage:
   9 #   STDIN:  stream containing one or more BLAST or PSI-BLAST reports.
  10 #   STDOUT: Raw alignment data for each HSP of each hit (BLAST format)
  11 #   STDERR: Progress info and any errors.
  12 #
  13 # For more documentation about working with Blast result objects,
  14 # see docs for these modules:
  15 #   Bio::Search::Result::BlastResult
  16 #   Bio::Search::Hit::BlastHit
  17 #   Bio::Search::HSP::BlastHSP
  18 #
  19 # For more documentation about the PSI-Blast parser, see docs for
  20 #   Bio::SearchIO::psiblast
  21 #
  22 # Author: Steve Chervitz <sac@bioperl.org>
  23 #
  24 # TODO:
  25 #   * Implement a Bio::SearchIO::Writer::HSPTextWriter object
  26 #     that can do this. Then this example can fit into the standard
  27 #     model used by the other writer examples in which a writer
  28 #     object is created and hooked up with a SearchIO output object.
  29
  30 use strict;
  31
  32
  33 use Bio::SearchIO;
  34
  35 # In this case, we only want raw alignments, and we only need to screen
  36 # on significance info (E- or P-value) so we don't need
  37 # to do a full parse of the alignments. Thus, we're using a -shalow_parse
  38 # flag to indicate that we don't need to parse alignments. This should
  39 # result in faster processing.
  40 # TODO: Convert this to use -format='blast'. Shallow-parse option not supported there.
  41 my $in = Bio::SearchIO->new(-format => 'psiblast',
  42                             -fh => \*ARGV,
  43                             -signif => 0.1,
  44                             -shallow_parse => 1,
  45                             -hold_raw_data => 1 );
  46
  47 while ( my $result = $in->next_result() ) {
  48   print STDERR "\nBLAST Results for $result\n\n";
  49   my $count = 0;
  50   foreach( $result->hits ) {
  51     print "Alignment for hit #", ++$count, "\n\n";
  52     print $_->raw_hit_data();
  53   }
  54   print "=" x 50 , "\n";
  55 }
  56
  57 printf STDERR "\n%d Blast report(s) processed.\n", $in->result_count;
  58