Bio::Tools::Analysis::Protein::Mitoprot - a wrapper around Mitoprot server
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); }
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:
The raw text of the program output
my $rawdata = $analysis_object->result;
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.
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.
Bio::SimpleAnalysisI, Bio::Tools::Analysis::SimpleAnalysisBase, 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:
http://bugzilla.open-bio.org/
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 _
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:
Returns the raw ASCII data stream but without HTML tags
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.
hash references of parsed results { input_length =>, basic_aas=>, acidic_aas=>, export_prob=>, charge=>, cleavage_site=>}.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.