examples/searchio/resultwriter.pl

   1 #!/usr/bin/perl
   2
   3 # Demonstrates the use of a SearchIO Blast parser and a SearchWriterI object
   4 # for producing tab-delimited output of result data from a Blast report
   5 # input stream.
   6 #
   7 # This writer only outputs information at the level of the result object.
   8 # This shows that you can work with a writer that only knows about
   9 # Bio::Search::Result objects and doesn't care about hit or HSP data.
  10 # Therefore, the output from this example doesn't contain any information
  11 # about hits or HSPs.
  12 # See the hitwriter.pl and hspwriter.pl examples for that.
  13 #
  14 # This parser represents a new and improved version of Bio::Tools::Blast.
  15 #
  16 # Usage:
  17 #   STDIN:  stream containing one or more BLAST or PSI-BLAST reports.
  18 #   STDOUT: none, but generates an output file "resultwriter.out"
  19 #           containing tab-delimited data on a per-report basis.
  20 #   STDERR: Any errors that occurred.
  21 #
  22 # For more documentation about the writer, including
  23 # a complete list of columns, see the docs for
  24 #   Bio::SearchIO::Writer::ResultTableWriter.
  25 #
  26 # For more documentation about working with Blast result objects,
  27 # see docs for these modules:
  28 #   Bio::Search::Result::BlastResult
  29 #   Bio::Search::Iteration::IterationI
  30 #   Bio::Search::Hit::BlastHit
  31 #   Bio::Search::HSP::BlastHSP
  32 #
  33 # For more documentation about the Blast parser, see docs for
  34 #   Bio::SearchIO
  35 #
  36 # Author: Steve Chervitz <sac@bioperl.org>
  37
  38
  39 use strict;
  40 use lib '../../';
  41
  42 use Bio::SearchIO;
  43 use Bio::SearchIO::Writer::ResultTableWriter;
  44 use Bio::SearchIO::Writer::HTMLResultWriter;
  45
  46 print "\nUsing SearchIO->new()\n";
  47
  48
  49 # Note that all parameters for the $in, $out, and $writer objects are optional.
  50 # Default in = STDIN; Default out = STDOUT; Default writer = all columns
  51 # In this example, we're reading from STDIN and  writing to STDOUT
  52 # and using the default columns for the writer.
  53 # We're also telling the script to timeout if input isn't received
  54 # within 10 sec. (Note the clock is still ticking when you background the job.)
  55 # Setting verbose to 1 is useful for debugging.
  56 my $in = Bio::SearchIO->new( -format => 'blast',
  57                              -fh => \*ARGV,
  58                              -signif => 0.1,
  59                              -verbose => 0,
  60                              -timeout_sec => 10 );
  61 # not specifying any columns to get the default.
  62 my $writer = Bio::SearchIO::Writer::ResultTableWriter->new();
  63 my $out    = Bio::SearchIO->new( -format => 'blast',
  64                                  -writer => $writer,
  65                                  -file => ">resultwriter.out");
  66
  67 my $writerhtml = new Bio::SearchIO::Writer::HTMLResultWriter();
  68 my $outhtml = new Bio::SearchIO(-writer => $writerhtml,
  69                                 -file   => ">searchio.html");
  70
  71
  72 while ( my $result = $in->next_result() ) {
  73     eval {
  74         # printf STDERR "Report %d: $result\n", $in->result_count;
  75         $out->write_result($result, ($in->result_count - 1 ? 0 : 1) );
  76
  77         $outhtml->write_result($result, 1);
  78
  79         # To get at the statistical parameters:
  80         # Calling raw_statistics() returns a list containing the
  81         # unparsed lines of the parameters section of the report.
  82         # Here we're only interested in parameters beginning with "effective".
  83         #         print "Report Stats, effective data:\n";
  84         #         foreach( $result->raw_statistics) {
  85         #             print "$_" if /^effective/i;
  86         #         }
  87
  88         ## For a simple progress monitor, uncomment this line:
  89         #print STDERR "."; print STDERR "\n" if $in->result_count % 50 == 0;
  90     };
  91     if($@) {
  92         warn "Warning: Blast parsing or writing exception caught for $result:\n$@\n";
  93     }
  94 }
  95
  96 printf STDERR "\n%d Blast report(s) processed.\n", $in->result_count;
  97 printf STDERR "Output sent to file: %s\n",  $out->file if $out->file;