NAME

Prints - Indexes Prints datafile


SYNOPSIS

  use Index::Prints;


DESCRIPTION

  This package is used to index Prints datafiles (prints.pval).
  It indexes the file by the accession number (gx; xxx) and by name (gc; xxx).
  #gc; 11SGLOBULIN
  #gx; PR00439
  #gn; 7
  #gi; 11-S seed storage protein family signature
  #gm; 74
  #mx; 11SGLOBULIN1
  #mi; Glutelin 2 motif I - 2
  #ml; 18
  #mc; 74
  #mn; 1
  #ls; 12
  #hs; 618
  #li; 12
  #hi; 618
  #A 0    1    0    6    14   0    3    6    0    62   0    0    0    0    1    0    53   0    
  #B 0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    
  #C 0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    
  #D 0    4    0    0    28   16   0    4    8    0    72   0    0    0    0    6    0    0    
  #E 0    22   0    0    9    0    0    6    5    0    1    0    0    0    0    4    0    0    
  #F 0    0    1    1    0    0    0    0    0    0    0    10   12   0    0    0    0    0    
  #G 0    0    0    0    17   0    0    0    0    1    0    0    0    0    0    3    12   74   
  #H 10   12   1    0    1    0    0    0    5    0    0    0    1    1    0    0    0    0    
  #I 0    0    0    52   0    0    0    1    0    0    0    16   0    0    0    0    0    0    
  #J 0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    
  #K 9    3    0    0    0    1    0    5    1    0    0    0    0    9    0    7    0    0    
  # ...
  # examples here
  use Index::Prints;
  my($res, $msg, $index);
  ($res, $index) = new Index::Prints($file); #Prints file to index
  die $index unless $res;
  #This input record delimeter is used when retrieving an entry from a file.
  ($res, $msg) = $index->setRecDel('dumper', '\ngc;/');
  die($msg) unless($res);
  #This input record delimeter is used during the building of the index file. It reads the file line by line
  #and need a specific pattern to record the position in the file.
  ($res, $msg) = $index->setRecDel('building', 'll;');
  die($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 $id = 'PR00439';
  my ($res, $pos) = $index->getIndex($id); #return the position in the file for 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 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 entry.
  $name = $name->[0] if $name;
  my ($res, $name) = $index->getField(['ac', 'name', 'desc']); #return the ac, name and description of this entry.
  if($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 entry.
  $name = $name->[0] if $name;
  #or simplier
  my ($res, $name) = $index->getField('name', \$entry); #return the name of this entry by parsing it on the fly
  $name = $name->[0] if $name;


VERSIONS

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

Copyright (c) European Bioinformatics Institute 2004


AUTHORS / ACKNOWLEDGEMENTS

Emmanuel Quevillon <tuco@ebi.ac.uk>

new

 Description:  Create a new object Index::HMM.
 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