debian man page for bio::seqio::flybase_chadoxml

Query: bio::seqio::flybase_chadoxml

OS: debian

Section: 3pm

Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar

Bio::SeqIO::flybase_chadoxml(3pm)			User Contributed Perl Documentation			 Bio::SeqIO::flybase_chadoxml(3pm)

NAME
Bio::SeqIO::flybase_chadoxml - FlyBase variant of chadoxml with sequence output stream
SYNOPSIS
It is probably best not to use this object directly, but rather go through the SeqIO handler system: $writer = Bio::SeqIO->new(-file => ">chado.xml", -format => 'flybase_chadoxml'); # assume you already have Sequence or SeqFeature objects $writer->write_seq($seq_obj); #after writing all seqs $writer->close_chadoxml();
DESCRIPTION
This is a simple subclass of Bio::SeqIO::chadoxml; please see its documentation for details.
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://redmine.open-bio.org/projects/bioperl/ AUTHOR - Peili Zhang Email peili@morgan.harvard.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ return_ftype_hash Title : return_ftype_hash Usage : $obj->return_ftype_hash() Function : A simple hash where returning it has be factored out of the main code to allow subclasses to override it. Returns : A hash that indicates what the name of the SO term is and what the name of the Sequence Ontology is in the cv table. Args : The string that represents the SO term. Status : return_reltypename Title : return_reltypename Usage : $obj->return_reltypename Function : Return the appropriate relationship type name depending on the feature type (typically part_of, but derives_from for polypeptide). Returns : A relationship type name. Args : A SO type name. Status : write_seq Title : write_seq Usage : $stream->write_seq(-seq=>$seq, -seq_so_type=>$seqSOtype, -src_feature=>$srcfeature, -src_feat_type=>$srcfeattype, -nounflatten=>0 or 1, -is_analysis=>'true' or 'false', -data_source=>$datasource) Function: writes the $seq object (must be seq) into chadoxml. Returns : 1 for success and 0 for error Args : A Bio::Seq object $seq, optional $seqSOtype, $srcfeature, $srcfeattype, $nounflatten, $is_analysis and $data_source. Overrides Bio::SeqIO::chadoxml's write_seq method just to add an internal close_chadoxml (mimics original use by FlyBase). perl v5.14.2 2012-03-02 Bio::SeqIO::flybase_chadoxml(3pm)
Related Man Pages
bio::seqio::flybase_chadoxml(3pm) - debian
bio::seqio::interpro(3pm) - debian
bio::seqio::metafasta(3pm) - debian
bio::seqio::swissdriver(3pm) - debian
bio::seqio::ztr(3pm) - debian
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