NAME

Bio::SeqIO::tinyseq::tinyseqHandler - XML event handlers to support NCBI TinySeq XML parsing

SYNOPSIS

Do not use this module directly; use the SeqIO handler system:

  $stream = Bio::SeqIO->new( -file => $filename, -format => 'tinyseq' );

  while ( my $seq = $stream->next_seq ) {
    ....
  }

DESCRIPTION

This object provides event handler methods for parsing sequence files in the NCBI TinySeq XML format. A TinySeq is a lightweight XML file of sequence information on one or more sequences, analgous to FASTA format.

See <https://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.mod.dtd> for the DTD.

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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR

Donald Jackson, <donald.jackson@bms.com>

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

  Title         : new
  Usage         : $handler = Bio::SeqIO::tinyseq::tinyseqHandler->new()
  Function      : instantiates a tinyseqHandler for use by
                  XML::Parser::PerlSAX
  Returns       : Bio::SeqIO::tinyseq::tinyseqHandler object
  Args          : NONE

start_document

  Title         : start_document
  Usage         : NONE
  Function      : start_document handler for use by XML::Parser::PerlSAX
  Returns       : NONE
  Args          : NONE

end_document

  Title         : end_document
  Usage         : NONE
  Function      : end_document handler for use by XML::Parser::PerlSAX
  Returns       : NONE
  Args          : NONE

start_element

  Title         : start_element
  Usage         : NONE
  Function      : start_element handler for use by XML::Parser::PerlSAX
  Returns       : NONE
  Args          : NONE

end_element

  Title         : end_element
  Usage         : NONE
  Function      : end_element handler for use by XML::Parser::PerlSAX
  Returns       : NONE
  Args          : NONE

characters

  Title         : characters
  Usage         : NONE
  Function      : characters handler for use by XML::Parser::PerlSAX
  Returns       : NONE
  Args          : NONE

TSeq

  Title         : TSeq
  Usage         : NONE
  Function      : event handler for END of a TSeq element
  Returns       : loh of parsed sequence atts for Bio::SeqIO::tinyseq
  Args          : NONE

_current_element

  Title         : _current_element
  Usage         : Internal method
  Function      : Utility method to return current element info
  Returns       : XML::Parser::PerlSAX hash for current element
  Args          : NONE