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NAME ^

Webservice::InterMine::Cookbook::Recipe6 - Advanced Results Management

SYNOPSIS ^

  # Get a list of Blast Matches, either 500 of them,
  # or ones with E-values over 8.0, whichever is the larger set

  use Webservice::InterMine ('www.flymine.org');

  my $query = Webservice::InterMine->new_query();

  # Specifying a name and a description is purely optional
  $query->name('Tutorial 6 Query');

  my ($subj, $obj, $evalue) = (qw/
      BlastMatch.subject.primaryIdentifier
      BlastMatch.object.primaryIdentifier
      BlastMatch.EValue
  /);

  $query->add_view($subj, $obj, $evalue);

  $query->set_sort_order($evalue => 'desc');

  my $ri = $query->results_iterator();

  # We need to check for errors here ourselves
  die $ri->status_line unless $ri->is_success;

  my @goodmatches;
  while (my $row = $ri->hashref) {
      if($row->{$evalue} >= 8 or @rows < 500) {
          push @goodmatches, [@{$row}{$subj, $obj}];
      }
  }

  $ri->close(); # good hygiene, as the iterator represents an open connection

DESCRIPTION ^

There are some limitations on the results you get back that are difficult to write as constraints, and can be more easily processed on the client side. The above example shows one of them - if we constrainted the e-value to be greater than 8, we might not get back 500 results, and if we specified 500 results as the result size, we might not get all the good matches.

But making sure we get all e-values over 8, or at least 500 results, is simple on the client side, and by using iteration you can apply filters of this sort to the stream of results, without having to keep all the results rows in memory or on file (you can simple throw away, or never even look at, results you don't want to keep). The example above is fairly simple, but you can perform any arbitrary logic on the result row to decide what you want to do with it.

For example, instead of just throwing away the bad matches, you could divide up the results into different result sets:

  while (my $row = $ri->hashref) {
      if ($row->{$evalue} >= 8) {
          push @good_matches, $row;
      }
      elsif ($row->{$evalue} >= 5) {
          push @dubious_matches, $row;
      else {
          push @bad_matches, $row;
      }
  }

or perform calculations on the data:

  my ($sum, $total);
  while (my $row = $ri->hashref) {
      $sum += $row->{$evalue};
      $total++;
  }
  my $average_evalue = $sum / $total;

obviously the possibilities depend on what you want the data for. Just like the results method, the ResultIterator object can return rows in one of three formats: string, arrayref and hashref.

There is no default - you must call one of these methods for each row you want back (you could even call different methods for different rows).

Whereas to unpack the results returned by the results operator we used the for operator, here we want to use the while operator with assignment in the brackets:

  while (my $row = $ri->$method) {
      # do something with the row...
  }

If you use Webservice::InterMine queries a lot, you may find yourself doing the same thing over and over in your code - this may be a sign that you can refactor out some of that repetition, instead of copy and pasting it between scripts. In the next recipe we examine ways to extend Webservice::InterMine to make it do what you want it to do.

CONCLUSION ^

As well as using the results method, you can get back the ResultsIterator directly to have fine-grained control over the results you get back, and what you want to do with them.

AUTHOR ^

Alex Kalderimis <dev@intermine.org>

BUGS ^

Please report any bugs or feature requests to dev@intermine.org.

SUPPORT ^

You can find documentation for this module with the perldoc command.

    perldoc Webservice::InterMine

You can also look for information at:

COPYRIGHT AND LICENSE ^

Copyright 2006 - 2010 FlyMine, all rights reserved.

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

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