Bio::Tools::Analysis::Protein ELM
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
 
Bio::Tools::Analysis::Protein::ELM
Package variables
Privates (from "my" definitions)
$ANALYSIS_SPEC = {name => 'ELM', type => 'Protein', version => 'n/a', supplier =>'BioComputing Unit, EMBL', description =>'Prediction of linear functional motifs in proteins', reference => 'NAR, 31:3625-3630'}
$URL = 'http://elm.eu.org/basicELM/cgimodel.py'
$ANALYSIS_NAME = 'ELM'
$INPUT_SPEC = [ { 'mandatory' => 'true', 'type' => 'Bio::PrimarySeqI', 'name' => 'seq', }, { 'mandatory' => 'false', 'type' => 'taxon_id or Bio::Species object', 'name' => 'species', 'default' => '9606', }, { 'mandatory' => 'false', 'type' => 'string', 'name' => 'compartment', 'default' => [1], }, ]
$RESULT_SPEC = { '' => 'bulk', 'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeature::Generic', 'parsed' => '{motif1_name=>{locus=>[], peptide=>[], regexp=>[] }, }', }
Included modules
Bio::SeqFeature::Generic
Bio::Tools::Analysis::SimpleAnalysisBase
HTML::HeadParser
HTTP::Request::Common qw ( POST )
IO::String
Inherit
Bio::Tools::Analysis::SimpleAnalysisBase
Synopsis
  # get a Bio::Seq object to start with, or a Bio::PrimaryI object.

  my $tool = Bio::Tools::Analysis::Protein::ELM->
      new(seq => $seqobj->primary_seq() );	
  $tool->compartment(['ER', 'Golgi']);
  $tool->species(9606);
  $tool->run;
  my @fts = $tool->Result('Bio::SeqFeatureI');
  $seqobj->addSeqFeature(@fts);
Description
This module is a wrapper around the ELM server (http://elm.eu.org/) which predicts short functional motifs on amino acid sequences. Two
filters can be applied to help limit the rate of false positives:
species and cellular compartment of the protein if known. The modules
supply methods for setting these attributes. To set species attribute,
use either a Bio::Species object or an NCBI taxon ID number. To set
the cell compartment attribute (any number of compartments can be
chosen) use an array reference to a list of compartment names.
Results can be obtained either as raw text output, as parsed into a
data structure, or as Bio::SeqFeature::Generic objects.
Methods
_init
No description
Code
compartmentDescriptionCode
speciesDescriptionCode
_run
No description
Code
resultDescriptionCode
_parse_raw
No description
Code
Methods description
compartmentcode    nextTop
 name        : compartment
 usage       : $elm->compartment(['golgi', 'er']);
 purpose     : get/setter for cell compartment specifications
 arguments   : None, single compartment string or ref to array of
                    compartment names.
 returns     : Array of compartment names (default if not previously
                    set).
speciescodeprevnextTop
 name      : species
 usage     : $tool->species('9606');
 purpose   : get/setter for species selction for ELM server
 arguments : none, taxon_id or Bio::Species object
 returns   : a string of the ncbi taxon_id
resultcodeprevnextTop
 name      : result
 usage     : $tool->result('Bio::SeqFeatureI');
 purpose   : parse results into sequence features or basic data format
 arguments : none    (retrieves raw text without html)
             a value (retrieves data structure)
             'Bio::SeqFeatureI' (returns array of sequence features)
					tag names are : {method=>'ELM', motif=>motifname,
                                     peptide => seqeunce of match,
                                     concensus=> regularexpression of match.
	.
 returns   : see arguments.
Methods code
_initdescriptionprevnextTop
sub _init {
    my $self = shift;
    $self->url($URL);
    $self->{'_ANALYSIS_SPEC'} = $ANALYSIS_SPEC;
    $self->{'_INPUT_SPEC'}    = $INPUT_SPEC;
    $self->{'_RESULT_SPEC'}   = $RESULT_SPEC;
    $self->{'_ANALYSIS_NAME'} = $ANALYSIS_NAME;
    return $self;
}
compartmentdescriptionprevnextTop
sub compartment {
    my ($self, $arg) = @_;
    if ($arg) {

        # convert to array ref if not one already
	if (ref ($arg) ne 'ARRAY') {
            $arg = [$arg];
	}
 
        ## now add params if valid
	for my $param (@$arg) {
            if (exists($cc{lc($param)})) {
                push @{$self->{'_compartment'}} , $cc{$param};
            } else {
                $self->warn("invalid argument ! Must be one of " .
                            join "\n", keys %cc );
            }
        }                       #end of for loop
			
    }                           #endif $arg
    return defined($self->{'_compartment'})? $self->{'_compartment'}
        : $self->input_spec()->[2]{'default'};
}
speciesdescriptionprevnextTop
sub species {
    my ($self, $arg) = @_;

    if ($arg) {
        if (ref($arg) && $arg->isa('Bio::Species')) {
            $self->{'_species'} = $arg->ncbi_taxid();
        } elsif ($arg =~ /^\d+$/) {
            $self->{'_species'} = $arg;
        } else {
            $self->warn("Argument must be a Bio::Species object or ". 
                        " an integer NCBI taxon id. ");
        }
    }                           #end if $arg
    return defined($self->{'_species'})?$self->{'_species'}
        :$self->input_spec()->[1]{'default'};
}
_rundescriptionprevnextTop
sub _run {
    my $self  = shift;
    $self->delay(1);
    # delay repeated calls by default by 3 sec, set delay() to change
    #$self->sleep;
    $self->status('TERMINATED_BY_ERROR');
	
    #### this deals with being able to submit multiple checkboxed
    #### slections

    #1st of all make param array
    my @cc_str;
    my @cmpts = @{$self->compartment()};
    for (my $i = 0; $i <= $#cmpts ; $i++) {
        splice @cc_str, @cc_str, 0,   'userCC',$cmpts[$i];
    }
    my %h = (swissprotId      => "",
             sequence         => $self->seq->seq,
             userSpecies      => '',
             typedUserSpecies => $self->species(),
             fun              => "Submit");
    splice (@cc_str, @cc_str,0, ( map{$_, $h{$_}} keys %h));

		
    my $request = POST $self->url(),
        Content_Type => 'form-data',
            Content  =>\@ cc_str;
    $self->debug( $request->as_string);
    my $r1 = $self->request($request);
    if ( $r1->is_error  ) {
	$self->warn(ref($self)." Request Error:\n".$r1->as_string);
	return;
    }

    my $text = $r1->content;
    my ($url) = $text =~ /URL=(\S+)\"/s; 
    $url =~ s/amp;//g ;
    my ($resp2);
    while (1) {
	my $req2 = HTTP::Request->new(GET=>$url);
	my $r2 = $self->request ($req2);
	if ( $r2->is_error ) {
	    $self->warn(ref($self)." Request Error:\n".$r2->as_string);	    
	    return;
	} 
	$resp2 = $r2->content();
	
	if ($resp2 !~ /patient/s) {
	    $self->status('COMPLETED');
	    $resp2=~ s/<[^>]+>/ /sg;
            $self->{'_result'} = $resp2;
	    return;
	} else {
	    print "." if $self->verbose > 0;
	    $self->sleep();
	}
    }
}
resultdescriptionprevnextTop
sub result {
    my ($self, $val) = @_;
    if ($val) {
        if (!exists($self->{'_parsed'}) ) {
            $self->_parse_raw();
        }
        if ($val eq 'Bio::SeqFeatureI') {
            my @fts;
            for my $motif (keys %{$self->{'_parsed'}}) {
                for (my $i = 0; $i< scalar @{$self->{'_parsed'}{$motif}{'locus'}};$i++) {
                    my ($st, $end) = split /\-/, $self->{'_parsed'}{$motif}{'locus'}[$i];
                    push @fts, Bio::SeqFeature::Generic->new 
                        (
                         -start       => $st,
                         -end         => $end,
                         -primary_tag => 'Domain',
                         -source      => 'ELM',
                         -tag   => {
                                    method    => 'ELM',
                                    motif     => $motif,
                                    peptide   => $self->{'_parsed'}{$motif}{'peptide'}[$i],
                                    concensus => $self->{'_parsed'}{$motif}{'regexp'}[0],
                                   });
                }
            }
            return @fts;
        }                       #end if BioSeqFeature
        return $self->{'_parsed'};
    }                           #endif ($val)
    return $self->{'_result'};
}
_parse_rawdescriptionprevnextTop
sub _parse_raw {
    my $self = shift;
    my $result = IO::String->new($self->{'_result'});
    my $in_results = 0;
    my $name;
    my %results;
    my $last;
    while (my $l = <$result>) {
        next unless  $in_results > 0 ||$l =~ /^\s+Elm\s+Name\s+Instances/;
        $in_results++;          #will be set whnstart of results reached.
        last if $l =~ /List of excluded/;
        next unless $in_results >1;

        my @line_parts = split /\s+/, $l;
        shift @line_parts;
        ## if result has motif name on 1 line
        if (scalar @line_parts == 1 && $line_parts[0]=~ /^\s*(\w+_\w+)/) {
            $name = $1;
            next;
        }
        ## else if is line with loci /seq matches
        elsif (@line_parts > 1) {
            my $index = 0;      ## array index
            my $read_loci = 0;  ## flag to know that loci are being read
            while ($index <= $#line_parts) {
                my $word = $line_parts[$index++];
                if ($read_loci ==0 && $word =~/_/) {
                    $name = $word;
                } elsif ($read_loci == 0 && $word =~ /^\w+$/ ) {
	            push @{$results{$name}{'peptide'}}, $word;
                } elsif ($word =~ /\d+\-\d+/) {
                    $read_loci = 1;
                    push @{$results{$name}{'locus'}}, $word;
                } else {        ## only get here if there are elements
                    last;
                }
            }                   #end of while
            push @{$results{$name}{'regexp'}}, $line_parts[$#line_parts];
        }                       #end of elsif

    }                           #end of while

    $self->{'_parsed'} =\% 	results;
}
General documentation
SEE ALSOTop
Bio::SimpleAnalysisI,
Bio::WebAgent
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                       - General discussion
  http://bio.perl.org/MailList.html           - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/
AUTHORSTop
Richard Adams, Richard.Adams@ed.ac.uk,
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _