Bio::Tools::Analysis::Protein::Mitoprot(3) a wrapper around Mitoprot

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.

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. 

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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, [email protected],

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=>}.

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