| Bio::SeqIO::tinyseq::tinyseqHandler(3pm) | User Contributed Perl Documentation | Bio::SeqIO::tinyseq::tinyseqHandler(3pm) |
Bio::SeqIO::tinyseq::tinyseqHandler - XML event handlers to support NCBI TinySeq XML parsing
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 ) {
....
}
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.
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
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.
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
Bio::SeqIO, Bio::Seq.
Donald Jackson, <donald.jackson@bms.com>
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : start_document Usage : NONE Function : start_document handler for use by XML::Parser::PerlSAX Returns : NONE Args : NONE
Title : end_document Usage : NONE Function : end_document handler for use by XML::Parser::PerlSAX Returns : NONE Args : NONE
Title : start_element Usage : NONE Function : start_element handler for use by XML::Parser::PerlSAX Returns : NONE Args : NONE
Title : end_element Usage : NONE Function : end_element handler for use by XML::Parser::PerlSAX Returns : NONE Args : NONE
Title : characters Usage : NONE Function : characters handler for use by XML::Parser::PerlSAX Returns : NONE Args : NONE
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
Title : _current_element Usage : Internal method Function : Utility method to return current element info Returns : XML::Parser::PerlSAX hash for current element Args : NONE
| 2020-10-28 | perl v5.30.3 |