NAME

InterPro - InterPro index utilities.


SYNOPSIS

  use Index::InterPro;


DESCRIPTION

  This package is used to index interpro.xml file.
  It indexes the database members accession number (see below 'dbkey="foo"').
  # examples here
  use Index::InterPro;
  my($res, $msg, $index);
  ($res, $index) = new Index::InterPro($file); #xml file here for interpro
  die $index unless $res;
  ($res, $msg) = $index->setRecDel('dumper', '</interpro>');
  die($msg) unless($res);
  ($res, $r_inx) = $index->buildIndex(['ac', 'name']); #list of entries you want to index. $regexp in this module for allowing rules.
  die($r_inx) unless($res);                            #if no argument given, will build the index with all the rules describe in $regexp.
  #or you can build the index on your own key-value pairs based on regular expression. Only the first match is taken into account.
  #so if you want to index multiple things based on the same line, you need to create another key-value pair.
  ($res, $r_inx) = $index->builIndex({ 'id' => '>(\S+)', 'name' => '^\s+\w+\s+(\S+)' });
  die $r_inx unless $res;
  ($res, $mess) = $index->indexOut($r_inx);               #need a reference to hash table.
  die $mess unless $res;
  my $id = 'IPR000342';
  my ($res, $pos) = $index->getIndex($id); #return the position in the file of the interpro entry containing this $id.
  die $pos unless $res;
  #getEntry returns a reference to an array in case of multiple entries found.
  my ($res, $entry) = $index->getEntry($id); #return the complete interpro entry.
  die $entry unless $res;
  $entry = $entry->[0] if($entry);
  #Either (parsing once the whole entry)
  my($res, $msg) = $index->parseFields(\$entry);
  die $msg unless $res;
  my ($res, $name) = $index->getField('name'); #return the name of this interpro entry.
  $name = $name->[0] if $name;
  my ($res, $name) = $index->getField(['ac', 'name', 'desc']); #return the ac, name and description of this interpro entry.
  if($name){
      my $nm = $name->[0];
      my $ac = $name->[1];
      my $de = $name->[2];
  }
  
  .... # see below for fields you can retrieve.
  my ($res, $name) = $index->get_name(); #return the name of this interpro entry.
  $name = $name->[0] if $name;
  #or simplier
  my ($res, $name) = $index->getField('name', \$entry); #return the name of this interpro entry by parsing it on the fly
  $name = $name->[0] if $name;
  my ($res, $goterms) = $index->get_goclass(\$entry); #return the GO annotations for this interpro entry.
  die $goterms unless $res;


VERSIONS

$Id: InterPro.pm.html,v 1.1.1.1 2005/08/18 13:18:25 hunter Exp $

Copyright (c) European Bioinformatics Institute 2002


AUTHORS / ACKNOWLEDGEMENTS

Emmanuel Quevillon <tuco@ebi.ac.uk>

new

 Description:  Create a new object Index::InterPro.
 Arguments:    $file a file to index
               $tool Do you want to use Dispatcher::Tool to use index.conf values? (optional)
 Returns:      1, $self on success
               0, msg on failure

_init

       Description: Initialize record delimiter, file and parse configuration file from index configuration file.
       Argument:    
       Returns:     1, '' on success
                    0, msg on error

get_goclass

 Description:  Retrieve GO terms tags for an InterPro entry.
 Arguments:
 Returns:      1, reference to an array containing the go informations.
               0, msg on failure

getDBname

 Description:  Return the DB name corresponding to the Application
               given.
 Arguments:    $entry, reference to a scalar which is the complete entry
               returned by get_entry subroutine.
 Returns:      1, database name or unknown

getMethId

 Description:  Retrieve methods informations (acc & name) from an InterPro entry.
 Arguments:
 Returns:      1, reference to an array containing strings ('ac: name').
               0, msg on error