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:
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