Christopher Fields > BioPerl > Bio::SeqIO::nexml

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Module Version: 1.006924   Source  

NAME ^

Bio::SeqIO::nexml - NeXML sequence input/output stream

SYNOPSIS ^

Do not use this module directly. Use it via the Bio::SeqIO class.

DESCRIPTION ^

This object can transform Bio::Seq objects to and from NeXML format. For more information on the NeXML standard, visit http://www.nexml.org.

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 - Chase Miller ^

Email: chmille4@gmail.com

CONTRIBUTORS ^

Mark Jensen, maj@fortinbras.us Rutger Vos, rutgeraldo@gmail.com

APPENDIX ^

The 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 : L<Bio::Seq> object
 Args    : NONE

rewind

 Title   : rewind
 Usage   : $seqio->rewind
 Function: Resets the stream
 Returns : none
 Args    : none

doc

 Title   : doc
 Usage   : $treeio->doc
 Function: Returns the biophylo nexml document object
 Returns : Bio::Phylo::Project
 Args    : none or Bio::Phylo::Project object

write_seq

 Title   : write_seq
 Usage   : $stream->write_seq(@seq)
 Function: Writes the $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : Array of 1 or more L<Bio::PrimarySeqI> objects
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