Bio::Tools::Analysis::Protein::NetPhos(3pm) | User Contributed Perl Documentation | Bio::Tools::Analysis::Protein::NetPhos(3pm) |
Bio::Tools::Analysis::Protein::NetPhos - a wrapper around NetPhos server
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) }
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 <http://www.cbs.dtu.dk/services/NetPhos/>.
This the first implementation 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.
Bio::SimpleAnalysisI, Bio::WebAgent
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Please direct usage questions or support issues to the mailing list:
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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://github.com/bioperl/bioperl-live/issues
Richard Adams, Richard.Adams@ed.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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:
Usage : $job->threshold(...) Returns : The significance threshold of a prediction Args : None (retrieves value) or a value between 0 and 1. Purpose : Get/setter of the threshold to be sumitted for analysis.
2018-10-27 | perl v5.26.2 |