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
  31 use Bio::SearchIO;
  32 use Bio::SearchIO::Writer::HTMLResultWriter;
  33
  34 my $outfile = "searchio.html";
  35 my $file = shift or die "Usage: $0 <BLAST-report-file>\n       HTML output is saved to $outfile\n";
  36
  37 my $in = Bio::SearchIO->new( -format => 'blast',
  38                              -file => $file,  #comment this out to read STDIN
  39                              #-fh => \*ARGV,  #uncomment this to read from STDIN
  40                              -verbose => 0 );
  41
  42 my $writer = new Bio::SearchIO::Writer::HTMLResultWriter();
  43 my $out = new Bio::SearchIO(-writer => $writer,
  44                             -file   => ">$outfile");
  45
  46
  47 while ( my $result = $in->next_result() ) {
  48     eval {
  49         # printf STDERR "Report %d: $result\n", $in->result_count;
  50         $out->write_result($result, 1);
  51     };
  52     if($@) {
  53         warn "Warning: Blast parsing or writing exception caught for $result:\n$@\n";
  54     }
  55 }
  56
  57 printf STDERR "\n%d Blast report(s) processed.\n", $in->result_count;
  58 printf STDERR "Output sent to file: %s\n",  $out->file if $out->file;