Bio::Tools::Analysis::Protein Mitoprot
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
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Summary
Bio::Tools::Analysis::Protein::Mitoprot - a wrapper around Mitoprot
server
Package variables
Privates (from "my" definitions)
$ANALYSIS_SPEC = { 'name' => 'Mitoprot', 'type' => 'Protein', 'version' => '1.0a4', 'supplier' => 'Munich Information Center for ProteinSequences', 'description' => 'mitochondrial sig seq prediction', }
$URL = 'http://ihg.gsf.de/cgi-bin/paolo/mitofilter?'
$MIN_LEN = 60
$ANALYSIS_NAME = "Mitoprot"
$INPUT_SPEC = [ { 'mandatory' => 'true', 'type' => 'Bio::PrimarySeqI', 'name' => 'seq', }, ]
%STATUS = map { $_ => 1 } qw(CREATED COMPLETED TERMINATED_BY_ERROR)
$RESULT_SPEC = { '' => 'raw text results', 'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeature::Generic', 'all' => 'hash of results', }
Included modules
Bio::SeqFeature::Generic
Bio::SeqIO
HTTP::Request::Common qw ( GET )
IO::String
Inherit
Bio::Tools::Analysis::SimpleAnalysisBase
Synopsis
  use Bio::Tools::Analysis::Protein::Mitoprot;
use Bio::PrimarySeq; my $seq = Bio::PrimarySeq->new (-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL', -primary_id=>'test'); # a Bio::PrimarySeqI object my $mitoprot = Bio::Tools::Analysis::Protein::Mitoprot->new ( -seq => $seq ); # sequence must be >!5aa long and start with an M. # run Mitoprot prediction on a DNA sequence my $mitoprot->run(); die "Could not get a result" unless $mitoprot->status =~ /^COMPLETED/; print $mitoprot->result; # print raw prediction to STDOUT foreach my $feat ( $mitoprot->result('Bio::SeqFeatureI') ) { # do something to SeqFeature # e.g. print as GFF print $feat->gff_string, "\n"; # or store within the sequence - if it is a Bio::RichSeqI $seq->add_SeqFeature($feat); }
Description
This class is a wrapper around the Mitoprot web server which
calculates the probability of a sequence containing a mitochondrial
targetting peptide. See http://mips.gsf.de/cgi-bin/proj/medgen/mitofilter for more details.
The results can be obtained in 3 formats:
   1
   The raw text of the program output
  my $rawdata = $analysis_object->result;
   2
   An reference to a hash of scores :
  my $data_ref = $analysis_object->result('parsed'); print "predicted
export prob is $data_ref->{'export_prob'}\n"; #
   key values of returned hash are input_length, basic_aas, acidic_aas,
export_prob, charge, cleavage_site.
   3
   A Bio::SeqFeature::Generic object
  my $ft = $analysis_object->result(Bio::SeqFeatureI);
print "export prob is ", ($ft->each_tag_value('export_prob'))[0] ,"\n";
   This the second implentation of Bio::SimpleAnalysisI which hopefully
will make it easier to write wrappers on various services. This class
uses a web resource and therefore inherits from Bio::WebAgent.
Methods
resultDescriptionCode
_init
No description
Code
_process_arguments
No description
Code
_run
No description
Code
Methods description
resultcode    nextTop
 Usage   : $job->result (...)
Returns : a result created by running an analysis
Args : various
The method returns a result of an executed job. If the job was
terminated by an error the result may contain an error message instead
of the real data.
This implementation returns differently processed data depending on
argument:
   undef
   Returns the raw ASCII data stream but without HTML tags
   'Bio::SeqFeatureI'
   The argument string defines the type of bioperl objects returned in an
array. The objects are Bio::SeqFeature::Generic. Feature primary
tag is "SigSeq". Feature tags are input_length , basic_aas,
acidic_aas, export_prob, charge, cleavage_site, method.
   'parsed'
   hash references of parsed results { input_length =>, basic_aas=>,
acidic_aas=>, export_prob=>, charge=>, cleavage_site=>}.
Methods code
resultdescriptionprevnextTop
sub result {
    my ($self,$value) = @_;
    #make sec feat of above threshold scores #
my @sig_pdctns; my @fts; if ($value ) { my $result = IO::String->new($self->{'_result'}); my %results; while (my $line = <$result>) { #make array of all scores or threshold depending on $value
next unless $line =~ /\d/ || $line =~ /^Cle/; if ($line =~ /^Net[^+\-\d]+ # Net, then anything except +,- or digit
((\+|-)?\d+)/x
) #then get charge with optional + or -
{ $results{'charge'} = $1; } elsif ($line =~ /^Input[^\d]+(\d+)/ ) { $results{'input_length'} = $1; } elsif ($line =~ /basic[^\d]+(\d+)$/ ) { $results{'basic_aas'} = $1; } elsif ($line =~ /acidic[^\d]+(\d+)$/) { $results{'acidic_aas'} = $1; } elsif ($line =~ /^Cleavage[^\d]+(\d+)$/) { $results{'cleavage_site'} = $1; } elsif ($line =~ /^Cleavage/) { $results{'cleavage_site'} = 'not predictable'; } elsif ($line =~ /^of export[^\d]+((0|1)\.\d+)$/) { $results{'export_prob'} = $1; } } if ($value eq 'Bio::SeqFeatureI') { push @fts, Bio::SeqFeature::Generic->new ( -start => 1, -end => ($results{'cleavage_site'} =~ /^\d+$/)?$results{'cleavage_site'}:$self->seq->length, -source => 'Mitoprot', -primary => 'Region', -tag =>{ export_prob => $results{'export_prob'}, charge => $results{'charge'}, basic_aas => $results{'basic_aas'}, acid_aas => $results{'acidic_aas'}, region_name => 'Transit_peptide', method => 'MitoProt', cleavage_site => $results{'cleavage_site'}, }, ); return @fts; #return Bioseqfeature array
} ## convert parsed data into a meta array format
else { return\% results; # hash based results ref
} } return $self->{'_result'};
}
_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_SPEC->{'name'};
    return $self;
}
_process_argumentsdescriptionprevnextTop
sub _process_arguments {
    #extra checking for sequence length
#mitoprot specific argument testing
my ($self, $args) = @_; #use base checking for existence of mandatory fields
$self->SUPER::_process_arguments($args) ; #then check specifics
$self->throw ("1st_aa must be M") if $self->seq->subseq(1,1) !~ /M/i; $self->throw ("sequence must be at least 15aa long") if $self->seq->length< 15; return;
}
_rundescriptionprevnextTop
sub _run {
    #request submitted by get not by post
my $self = shift; $self->delay(1); $self->sleep; $self->status('TERMINATED_BY_ERROR'); my $url = $self->url . "seq=".lc($self->seq->seq). "&seqnam="; my $request = GET $url; my $content = $self->request($request); my $text = $content->content; #1st reponse
#remove html stuff
$text =~ s/.*<PRE>(.*)<\/PRE>.*/$1/s; $text =~ s/<[^>]+>//sg; $self->status('COMPLETED') if $text ne '' && $self->seq->length > $MIN_LEN; $self->{'_result'} = $text; } 1;
}
General documentation
SEE ALSOTop
Bio::SimpleAnalysisI,
Bio::Tools::Analysis::SimpleAnalysisBase,
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
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.
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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
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 _