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Summary

Bio::Tools::Analysis::Protein::ELM - a wrapper around the ELM server which predicts short functional motifs on amino acid sequences

Package variables

Included modules

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.
False positives can be limited by providing values for the species
and cellular compartment of the protein. To set the 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, parsed into a
data structure, or as Bio::SeqFeature::Generic objects.

Methods

Methods description

 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).

 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

 name      : result
 usage     : $tool->result('Bio::SeqFeatureI');
 purpose   : parse results into sequence features or basic data format
 arguments : 1. none    (retrieves raw text without html)
             2. a value (retrieves data structure)
             3. 'Bio::SeqFeatureI' (returns array of sequence features)
                tag names are : {method => 'ELM', motif => motifname,
                                 peptide => seqeunce of match,
                                 concensus => regexp of match}.
 returns   : see arguments.

Methods code

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;

}

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'};

}

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'};

}

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      => $self->species,
             typedUserSpecies => '',
             fun              => "Submit");
    splice (@cc_str, @cc_str,0, ( map{$_, $h{$_}} 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) = $text =~ /URL=\S+(fun=\S+r=\d)/s;
    #$url =~ s/amp;//g ;
    my ($resp2);
    $url = $URL . "?" .$url;
    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(1);
	}
    }

}

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'};
}

## internal sub to parse raw data into internal data structure which is cached.

}

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;
}
1;

}

General documentation

Bio::SimpleAnalysisI,
Bio::WebAgent

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
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Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:

  https://redmine.open-bio.org/projects/bioperl/

Richard Adams, Richard.Adams@ed.ac.uk,

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _