NAME

Hmmer - Hmmer utilities.


SYNOPSIS

  # examples here
  use Dispatcher::Tool::Hmmer;


DESCRIPTION


VERSIONS

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

Copyright (c) European Bioinformatics Institute 2002


AUTHORS / ACKNOWLEDGEMENTS

Ville Silventoinen <vsi@ebi.ac.uk> Emmanuel Quevillon <tuco@ebi.ac.uk>

new

 Description: Constructor allocates an anonymous hash, which
              is tied to the class.
 Arguments:   $name        Hmmer tool name (optional). If given, sets the
                           Dispatcher::Config object automatically inside
                           the object. If not given, the Dispatcher::Config
                           must be set later with setConfig.
              $defaults    Default values for configuration, hash reference
                           (optional).
 Returns:     $self object

getCmdLine

 Description: Returns Hmmer command line.
 Arguments:   -
 Returns:     1, cmd on success
              0, msg on failure

parseResult

 Description: Reads a Hmmer result file and creates a hash table:
              nhits       => '2',
              '1'         => { seqid       => 'Y902_MYCTU',
                               ndomains    => '3',
                               '1'         => { methid => 'PF00672',
                                                desc   => 'HAMP domain',
                                                start  => '151',
                                                end    => '219',
                                                score  => '46.9',
                                                evalue => '4.3e-11'
                                              },
                               '2'         => { methid => 'PF00512',
                                                desc   => 'His Kinase A (phosphoacceptor) domain',
                                                start  => '230',
                                                end    => '296',
                                                score  => '55.8',
                                                evalue => '9.2e-14'
                                              },
                               '3'         => { methid => 'PF02518',
                                                desc   => 'Histidine kinase-, DNA gyrase B-, and HSP90',
                                                start  => '338',
                                                end    => '445',
                                                score  => '105.6',
                                                evalue => '9.6e-29'
                                              },
                             },
              '2'         => { seqid       => 'WAP_RAT',
                               ...
                             }
 Arguments:   $href          Reference to a hash.
              $result        Path to a Hmmer result file.
              $inx           Reference to a hash.
 Returns:     1, ''  on success
              0, msg on failure

doSmartFilter

 Description: Perform a filtering on Smart results. Need smart.thresholds & smart.desc files (not public)
 Argument:    $hitac  the accesion number of the hit
 Returns:     1 on success

getRawResult

 Description: Returns raw formatted result string.
 Arguments:   $href      Reference to a result hash.
              $seqs      Sequence hash (see InterProScan::checkSequences).
              $iprscan   Reference to Dispatcher::Tool::InterProScan object.
                         Required for IPR fields and GO terms.
              $ipr       1: add IPR fields
                         0: no (default)
              $go        1: add GO terms
                         0: no (default)
 Returns:     1, str on success
              0, msg on failure

filterID

       Description: Filter out the id depending on the application rule.
                    Pfam uses version number at the end of the accession number
                    like (PFXXXXX.4). So '.4' breaks the link to pfam website.
       Arguments:   $id The id to filer out.
                    $appl Application name to know how to filter the id.
       Returns:     1, filter id on success
                    0, msg on error

areFromSameClan

    Description: Get Pfam entries and check if they belong to the same clan.
    Arguments:   $hash Reference to oa hash table containing parsed results from Pfam
    Returns:     1, $hash Hash table with removed overlaps if found and from the same clan.
                 0  '' on error

removeOverlap

 Description: Used when 2 Pfam ids are in the same clan and overlap. Remove the hit with the lowest score.
 Arguments:   $hash  Hash table containing hits for a protein.
              $id1  Key number (domain number)
              $id2  Key number (domain number)
 Returns:     1, Key number to be removed.
              0, $msg on error

hasNestedDomain

    Description: Check if two overlapping PFam hits are related by any nested rule.
    Arguments:   $domain1  PFam accession
                 $domain2  PFam accession to check if nested domain for $domain1
    Returns:     1, 1  if $domain2 nested domain of $domain1
                 1, '' if not