Summary

Bio::Tools::Analysis::Protein::Sopma - a wrapper around
Sopma protein secondary structure prediction server

Package variables

Included modules

Inherit

Bio::Tools::Analysis::SimpleAnalysisBase

Synopsis

  use Bio::Tools::Analysis::Protein::Sopma;
  #get a Bio::Seq or Bio::PrimarySeq
  my $seq;

  my $sopma = Bio::Tools::Analysis::Protein::Sopma->new
      (-seq=>$seq, states=>4);
  $sopma->run;
  print $sopma->result;# #raw text to standard error

Description

A module to remotely retrieve predictions of protein secondary
structure. Each residue in the protein receives a score representing
the likelihood of existing in each of four different states (helix,
coil, turn or sheet), e.g.,

  my $analysis_object = Bio::Tools::SimpleAnalysis::Protein::Sopma->new
      ( -seq          => $seq,
        -states       =>4,
        -window_width =>15,
      );

creates a new object. Compulsory arguments -seq. Optional arguments
-states, -window_width,-similarity_threshold. These values can also be
set by direct methods , e.g.,

  $analysis_object->states(4);
  $analysis_object->run   ;

submits the query to the server and obtains raw text output Given an
amino acid sequence the results can be obtained in 4 formats,
determined by the argument to the result method
    The raw text of the program output

  my $rawdata = $analysis_object->result;

    A reference to an array of hashes of scores for each state and the
assigned state.

  my $data_ref = $analysis_object->result('parsed');
  print "score for helix at residue 2 is $data_ref->[1]{'helix'}\n";
  print "predicted struc  at residue 2 is $data_ref->[1]{'struc}\n";
Hash keys are 'helix', 'struc', 'sheet', 'coil', 'turn'.

    An array of Bio::SeqFeature::Generic objects where each feature is a
predicted unit of secondary structure. Only stretches of helix/sheet
predictions for longer than 4 residues are defined as helices/sheets.

  my @fts = $analysis_object->result(Bio::SeqFeatureI);
  for my $ft (@fts) {
      print " From ",  $ft->start, " to  ",$ft->end, " struc: " ,
             ($ft->each_tag_value('type'))[0]  ,"\n";
  }

    A Bio::Seq::Meta::Array implementing sequence.
    This is a Bio::Seq object that can also hold data about each residue
in the sequence. In this case, the sequence can be associated with a
arrays of Sopma prediction scores. e.g.,

  my $meta_sequence = $analysis_object->result('meta');
  print "scores from residues 10 -20 are ",
      $meta_sequence->named_submeta_text("Sopma_helix",10,20), "\n";

    Meta sequence names are : Sopma_helix, Sopma_sheet, Sopma_turn,
Sopma_coil, Sopma_struc, representing the scores for each residue.
    Many methods common to all analyses are inherited from
Bio::Tools::Analysis::SimpleAnalysisBase.

Methods

Methods description

  Useage  : $job->similarity_threshold(...)
  Returns : The  similarity threshold used in the analysis
  Args    : None (retrieves value) or  an integer (default = 8) 
            that sets the similarity threshold .

  Useage   : $job->window_width(...)
  Returns  : The  window width used in the analysis
  Args     : None (retrieves value) or  an integer (default = 17)
             that sets the window width.

  Useage   : $job->states(...)
  Returns  : The number of secondary structure prediction states
  Args     : None (retrieves value) or either '3' or '4' to set
             prior to running analysis.

  Usage   : $job->result (...)
  Returns : a result created by running an analysis
  Args    : various

Methods code

sub similarity_threshold {

    my ($self, $value) = @_;
    if ($value) {
        $self->throw ("similarity_threshold must be integer")
            unless $value =~ /^\d+$/;
        $self->{'_similarity_threshold'} = $value;
    }
    $self->{'_similarity_threshold'} ||= $self->input_spec->[1]{'default'};
    return $self->{'_similarity_threshold'};

}

sub window_width {

    my ($self, $value) = @_;
    if ($value) {
        $self->throw ("window_width must be integer")
            unless $value =~ /^\d+$/;
        $self->{'_window_width'} = $value;
    }
    $self->{'_window_width'} ||= $self->input_spec->[2]{'default'};
    $self->warn ("window width longer than sequence!")
        unless $self->{'_window_width'} < $self->seq->length;
    return $self->{'_window_width'};

}

sub states {

    my ($self, $value) = @_;
    if ($value) {
        $self->throw ("number of states must be 3 or 4")
            unless $value == 3 or $value ==4;
        $self->{'_states'} = $value;
    }
    $self->{'_states'} ||= $self->input_spec->[3]{'default'};
    return $self->{'_states'};

}

sub result {

    my ($self,$value, $run_id) = @_;

    my @score;
    my @fts;

    if ($value ) {
        if (!exists($self->{'_parsed'} )) {
            my $result = IO::String->new($self->{'_result'});
            while (my $line = <$result>) {
                next unless $line =~ /^[HCET]\s/; # or for sopma/hnn  /^[A-Z]\s/
                $line =~/^([A-Z])\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)/; # or for so
                push @score, { struc => $1,
                               helix => $2,
                               sheet => $3,
                               coil => $5,
                             };
                #include turn if 4states are requested
                $score[$#score]{'turn'} = $4 if $self->states == 4;
                #can optimize by duplicating code here
            }
            $self->{'_parsed'} =\@ score;
        }
        if ($value eq 'Bio::SeqFeatureI') {
            $self->_get_2ary_coords();
            for my $type (keys %{$self->{'_parsed_coords'}} ) {
                next if $type =~  /\w{2,}/; #if not H,C,E or T

				## these 2 are added to distinguish features on same
               ## sequence run with different params
				my $tag_hash = {
								type   => $type,
                                method => $self->analysis_name,
								};
				$self->_add_params_to_result($tag_hash);

				## now make feature object
                for my $loc (@{$self->{'_parsed_coords'}{$type}} ) {
                    push  @fts,   Bio::SeqFeature::Generic->new
                        (-start   => $loc->{'start'},
                         -end     => $loc->{'end'},
                         -source  => 'Sopma',
                         -primary => 'Domain',
                         -tag => $tag_hash,
                                 );
                }               #end of array of strucs of type
            }                   # end of all 2nd struc elements
            delete $self->{'_parsed_coords'}; #remove temp data
            return @fts;
        }                       #endif BioSeqFeature

        elsif ($value eq 'meta') {
            #1st of all make 3 or 4 arrays of scores for each type from column data
            my %type_scores;
            for my $aa (@{$self->{'_parsed'}}) {
                for my $type (qw(struc helix sheet  coil)) {
                    push @{$type_scores{$type}}, $aa->{$type};
                }
                push @{$type_scores{'turn'}}, $aa->{'turn'} if  exists $aa->{'turn'};
            }
			
			## convert to meta sequence array ##
			if (!$self->seq->isa("Bio::Seq::Meta::Array")) {
           		 bless ($self->seq, "Bio::Seq::Meta::Array");
				}
            $self->seq->isa("Bio::Seq::MetaI")
                || $self->throw("$self is not a Bio::Seq::MetaI");


            $Bio::Seq::Meta::Array::DEFAULT_NAME = 'Sopma_struc';
            for my $struc_type (keys %type_scores) {
                my $meta_name = "Sopma". "_" . "$struc_type";
				if ($run_id) {
					$meta_name .= "|$run_id";
				}
                my @meta = map{$_->{$struc_type}} @{$self->{'_parsed'}};
                if (grep{$_ eq $meta_name}$self->seq->meta_names >0) {
                    $self->warn ("$meta_name already exists , not overwriting!");
                    next;
                }
                $self->seq->named_meta($meta_name,\@meta );
            }
            # return  seq array object implementing meta sequence #
            return $self->seq;

        }
		## else return parsed data if $value is defined
		 else {
            return $self->{'_parsed'};
        }

    }                           #endif ($value)
    #return raw result if no return format stated
    return $self->{'_result'};

}

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 _get_2ary_coords {

    #helper sub for result;
    ##extracts runs of structure > MIN_STRUC_LENresidues or less if Turn:
    #i.e., helical prediction for 1 residue isn't very meaningful...
    ## and poulates array of hashes with start/end values.
    ##keys of $Result are 'H' 'T' 'C' 'E'. 
    my ($self) = @_;
    my @prot = @{$self->{'_parsed'}};
    my %Result;
    for (my $index = 0; $index <= $#prot; $index++) {

        my $type        = $prot[$index]{'struc'};
        next unless $type && $type =~ /[HTCE]/;
        my $length = 1;
        for (my $j = $index + 1; $j <= $#prot; $j++) {
            my $test = $prot[$j];
            if ($test->{'struc'} eq $type) {
                $length++;
            } elsif (  $length > MIN_STRUC_LEN  ||
                       ($length <= MIN_STRUC_LEN && $type eq 'T') ) {
                push @{$Result{$type}}, {start => $index + 1 ,  end => $j};
                $index += $length -1;
                last;
            } else {
                $index += $length - 1;
                last;
            }
        }
    }
    $self->{'_parsed_coords'} =\% Result; #temp assignment

}

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');
    my $request = POST 'http://npsa-pbil.ibcp.fr/cgi-bin/secpred_sopma.pl',
        Content_Type => 'form-data',
            Content  => [title     => "",
                         notice    => $self->seq->seq,
                         ali_width => 70,
                         states    => $self->states,
                         threshold => $self->similarity_threshold ,
                         width     => $self->window_width,
                        ];

    my $text = $self->request($request)->content;
    return $self unless $text;

    #### get text only version of results ## 
    my ($next) = $text =~ /Prediction.*?=(.*?)>/;
    my $out    = "http://npsa-pbil.ibcp.fr/". "$next";
    my $req2   = HTTP::Request->new(GET=>$out);
    my $resp2  = $self->request ($req2);
    $self->{'_result'} = $resp2->content;
    $self->status('COMPLETED') if $resp2 ne '';
    return $self;

}

sub _add_params_to_result {

	## called when making Seqfeature objects
	my ($self, $tag_hash) = @_;
	my $hash;
	## adds input parameter values to SeqFeatureI results where multiple
    ##  parameter values are possible. Only adds value if not default. 
	map{$hash->{$_->{'name'}} = $_}@{$self->input_spec()};

	for my $p (keys %$hash) {
		if (!ref($self->$p) && $self->$p ne $hash->{$p}{'default'}) {
			$tag_hash->{$p} = $self->$p;
		}
	}

}

General documentation

Bio::SimpleAnalysisI,
Bio::Tools::Analysis::SimpleAnalysisBase
Bio::Seq::Meta::Array,
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.

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  bioperl-bugs@bio.perl.org
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Richard Adams, Richard.Adams@ed.ac.uk,