Hmmer - Hmmer utilities.
# examples here use Dispatcher::Tool::Hmmer;
$Id: Hmmer.pm.html,v 1.1.1.1 2005/08/18 13:18:25 hunter Exp $
Copyright (c) European Bioinformatics Institute 2002
Ville Silventoinen <vsi@ebi.ac.uk> Emmanuel Quevillon <tuco@ebi.ac.uk>
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
Description: Returns Hmmer command line. Arguments: - Returns: 1, cmd on success 0, msg on failure
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
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
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
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
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
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
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