examples/searchio/htmlwriter.pl

   1 #!/usr/bin/perl
   2
   3 # Demonstrates the use of a SearchIO Blast parser and a SearchWriterI object
   4 # for producing HTML Blast output from a Blast report input stream.
   5 #
   6 # Usage:
   7 #   STDIN:  none; supply filename of BLAST report on command-line
   8 #   STDOUT: none; generates an output file "searchio.html"
   9 #           containing HTML-formatted Blast Report
  10 #   STDERR: Any errors that occurred.
  11 #
  12 # For more documentation about the writer, including
  13 # a complete list of columns, see the docs for
  14 #   Bio::SearchIO::Writer::HTMLResultWriter.
  15 #
  16 # For more documentation about working with Blast result objects,
  17 # see docs for these modules:
  18 #   Bio::Search::Result::BlastResult
  19 #   Bio::Search::Iteration::IterationI
  20 #   Bio::Search::Hit::BlastHit
  21 #   Bio::Search::HSP::BlastHSP
  22 #
  23 # For more documentation about the Blast parser, see docs for
  24 #   Bio::SearchIO
  25 #
  26 # Author: Steve Chervitz <sac@bioperl.org>
  27
  28
  29 use strict;
  30 use lib '../../';
  31
  32 use Bio::SearchIO;
  33 use Bio::SearchIO::Writer::HTMLResultWriter;
  34
  35 my $outfile = "searchio.html";
  36 my $file = shift or die "Usage: $0 <BLAST-report-file>\n       HTML output is saved to $outfile\n";
  37
  38 my $in = Bio::SearchIO->new( -format => 'blast',
  39                              -file => $file,  #comment this out to read STDIN
  40                              #-fh => \*ARGV,  #uncomment this to read from STDIN
  41                              -verbose => 0 );
  42
  43 my $writer = new Bio::SearchIO::Writer::HTMLResultWriter();
  44 my $out = new Bio::SearchIO(-writer => $writer,
  45                             -file   => ">$outfile");
  46
  47
  48 while ( my $result = $in->next_result() ) {
  49     eval {
  50         # printf STDERR "Report %d: $result\n", $in->result_count;
  51         $out->write_result($result, 1);
  52     };
  53     if($@) {
  54         warn "Warning: Blast parsing or writing exception caught for $result:\n$@\n";
  55     }
  56 }
  57
  58 printf STDERR "\n%d Blast report(s) processed.\n", $in->result_count;
  59 printf STDERR "Output sent to file: %s\n",  $out->file if $out->file;