Query: bio::seqio::kegg
OS: debian
Section: 3pm
Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar
Bio::SeqIO::kegg(3pm) User Contributed Perl Documentation Bio::SeqIO::kegg(3pm)NAMEBio::SeqIO::kegg - KEGG sequence input/output streamSYNOPSIS# It is probably best not to use this object directly, but # rather go through the SeqIO handler system. Go: use Bio::SeqIO; $stream = Bio::SeqIO->new(-file => $filename, -format => 'KEGG'); while ( my $seq = $stream->next_seq() ) { # do something with $seq }DESCRIPTIONThis class transforms KEGG gene records into Bio::Seq objects. Mapping of record properties to object properties This section is supposed to document which sections and properties of a KEGG databank record end up where in the Bioperl object model. It is far from complete and presently focuses only on those mappings which may be non-obvious. $seq in the text refers to the Bio::Seq::RichSeqI implementing object returned by the parser for each record. 'ENTRY' $seq->primary_id 'NAME' $seq->display_id 'DEFINITION' $seq->annotation->get_Annotations('description'); 'ORTHOLOG' grep {$_->database eq 'KO'} $seq->annotation->get_Annotations('dblink') 'CLASS' grep {$_->database eq 'PATH'} $seq->annotation->get_Annotations('dblink') 'POSITION' FIXME, NOT IMPLEMENTED 'PATHWAY' for my $pathway ( $seq->annotation->get_Annotations('pathway') ) { # } 'DBLINKS' $seq->annotation->get_Annotations('dblink') 'CODON_USAGE' FIXME, NOT IMPLEMENTED 'AASEQ' $seq->translate->seq 'NTSEQ' $seq-E<gt>seqFEEDBACKMailing 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://redmine.open-bio.org/projects/bioperl/ AUTHOR - Allen Day Email allenday@ucla.eduAPPENDIXThe rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq::RichSeq object Args : write_seq Title : write_seq Note : write_seq() is not implemented for KEGG format output. perl v5.14.2 2012-03-02 Bio::SeqIO::kegg(3pm)
Related Man Pages |
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