Bio::Tools::Analysis::UsereContributBio::Tools::Analysis::Protein::Mitoprot(3)NAMEBio::Tools::Analysis::Protein::Mitoprot - a wrapper around Mitoprot
server
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.
SEE ALSO
Bio::SimpleAnalysisI, Bio::Tools::Analysis::SimpleAnalysisBase,
Bio::WebAgent
FEEDBACK
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
Support
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 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/
AUTHORS
Richard Adams, Richard.Adams@ed.ac.uk,
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
result
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=>}.
perl v5.14.120Bio::Tools::Analysis::Protein::Mitoprot(3)
