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BioPerl-1.007002
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SeqIO::tinyseq::tinyseqHandler

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

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