Bio::SeqIO::tinyseq::tinyseqHandler.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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 <http://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:
   http://bugzilla.open-bio.org/
 
 

SEE ALSO

Bio::SeqIO, Bio::Seq.

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