# $Id: NetPhos.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::Tools::Analysis::Protein::NetPhos # # Please direct questions and support issues to # # Cared for by Heikki Lehvaslaiho # # Copyright Richard Adams # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Tools::Analysis::Protein::NetPhos - a wrapper around NetPhos server =head1 SYNOPSIS use Bio::Tools::Analysis::Protein::NetPhos; my $seq; # a Bio::PrimarySeqI object my $threshold = "0.90"; my $netphos = Bio::Tools::Analysis::Protein::NetPhos->new ( -seq => $seq, -threshold => $threshold ); # run NetPhos prediction on a sequence my $netphos->run(); # alternatively you can say $netphos->seq($seq)->threshold($threshold)->run; die "Could not get a result" unless $netphos->status =~ /^COMPLETED/; print $netphos->result; # print raw prediction to STDOUT foreach my $feat ( $netphos->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) } =head1 DESCRIPTION This class is wrapper around the NetPhos 2.0 server which produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins. See L. This the first 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. =head1 SEE ALSO L, L =head1 FEEDBACK =head2 Mailing Lists 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 =head2 Support Please direct usage questions or support issues to the mailing list: I 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. =head2 Reporting Bugs 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: http://bugzilla.open-bio.org/ =head1 AUTHORS Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Tools::Analysis::Protein::NetPhos; use vars qw($FLOAT); use strict; use IO::String; use Bio::SeqIO; use HTTP::Request::Common qw (POST); use Bio::SeqFeature::Generic; use base qw(Bio::Tools::Analysis::SimpleAnalysisBase); $FLOAT = '[+-]?\d*\.\d*'; my $URL = 'http://www.cbs.dtu.dk/cgi-bin/nph-webface'; my $ANALYSIS_SPEC = { 'name' => 'NetPhos', 'type' => 'Protein', 'version' => '2.0', 'supplier' => 'Center for Biological Sequence Analysis, Technical University of Denmark', 'description' => 'Prediction of serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins', }; my $INPUT_SPEC = [ { 'mandatory' => 'true', 'type' => 'Bio::PrimarySeqI', 'name' => 'seq', }, { 'mandatory' => 'false', 'type' => 'float', 'name' => 'threshold', 'default' => 0.8, } ]; my $RESULT_SPEC = { '' => 'bulk', # same as undef 'Bio::SeqFeatureI' => 'ARRAY of Bio::SeqFeeature::Generic', 'raw' => 'Array of [ position, score, residue ]' }; =head2 result Name : result Usage : $job->result (...) Returns : a result created by running an analysis Args : none (but an implementation may choose to add arguments for instructions how to process the raw result) The method returns a scalar representing a result of an executed job. If the job was terminated by an error the result may contain an error message instead of the real data (or both, depending on the implementation). This implementation returns differently processed data depending on argument: =over 3 =item undef Returns the raw ASCII data stream but without HTML tags =item 'Bio::SeqFeatureI' The argument string defined the type of bioperl objects returned in an array. The objects are L. =item anything else Array of array references of [ position, score, residue]. =back =cut sub result { my ($self,$value) = @_; my @predictions; my @fts; if ($value ) { my $result = IO::String->new($self->{'_result'}); while (<$result>) { next if /^____/; /^\S+ +(\d+) +\w+ +(0\.\d+) +.([STY])/; next unless $3 and $2 > $self->threshold; push @predictions, [$1, $2, $3]; } if ($value eq 'Bio::SeqFeatureI') { foreach (@predictions) { push @fts, Bio::SeqFeature::Generic->new (-start => $_->[0], -end => $_->[0] , -source => 'NetPhos', -primary => 'Site', -tag => { score => $_->[1], residue => $_->[2] }); } return @fts; } return \@predictions; } return $self->{'_result'}; } =head2 threshold Usage : $job->threshold(...) Returns : The significance threshold of a prediction Args : None (retrieves value) or a value beween 0 and 1. Purpose : Get/setter of the threshold to be sumitted for analysis. =cut sub threshold { my ($self,$value) = @_; if( defined $value) { if ( $value !~ /$FLOAT/ or $value < 0 or $value > 1 ) { $self->throw("I need a value between 0 and 1 , not [". $value. "]") } $self->{'_threshold'} = $value; return $self; } return $self->{'_threshold'} || $self->input_spec->[1]{'default'} ; } 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; } sub _run { my $self = shift; # format the sequence into fasta my $seq_fasta; my $stringfh = new IO::String($seq_fasta); my $seqout = Bio::SeqIO->new(-fh => $stringfh, -format => 'fasta'); $seqout->write_seq($self->seq); $self->debug($seq_fasta); # delay repeated calls by default by 3 sec, set delay() to change $self->sleep; $self->status('TERMINATED_BY_ERROR'); my $request = POST $self->url, Content_Type => 'form-data', Content => [configfile => '/usr/opt/www/pub/CBS/services/NetPhos-2.0/NetPhos.cf', SEQPASTE => $seq_fasta]; my $content = $self->request($request); my $text = $content->content; my ($result_url) = $text =~ /follow debug("url is $result_url\n\n"); my $ua2 = $self->clone; my $content2 = $ua2->request(POST $result_url); my $ua3 = $self->clone; $result_url =~ s/&.*//; $self->debug("final result url is $result_url\n"); my $content3 = $ua3->request(POST $result_url); #print Dumper $content3; my $response = $content3->content; $response =~ s/.*
(.*)<\/pre>.*/$1/s;
    $response =~ s/<.*?>//gs;

    $self->{'_result'} = $response;

    $self->status('COMPLETED') if $response ne '';

}

1;