NAME¶
Bio::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:
https://github.com/bioperl/bioperl-live/issues
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=>}.