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 reads and writes Bio::Seq objects to and from TinySeq XML format. A TinySeq is a lightweight XML file of sequence information, 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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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, <[email protected]>Parts of this module and the test script were patterned after Sheldon McKay's Bio::SeqIO::game. If it breaks, however, it's my fault not his ;).
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _next_seq
Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : NONE
write_seq
Title : write_seq Usage : $seq = $stream->write_seq(@sequence_objects); undef $stream Function: outputs one or more sequence objects as TinySeq XML Returns : 1 on success Args : one or more sequence objects as TinySeq XML
Because the TSeq dtd includes closing tags after all sets are written, the output will not be complete until the program terminates or the object is forced out of scope (see close_writer()). May not perfectly reproduce TSeq_sid element for all sequences
_get_seqs
Title : _get_seqs Usage : Internal function - use next_seq() instead Function: parses the XML and creates Bio::Seq objects Returns : 1 on success Args : NONE
Currently stores all sequence objects into memory. I will work on do more of a stream-based approach
_get_species
Title : _get_species Usage : Internal function Function: gets a Bio::Species object from cache or creates as needed Returns : a Bio::Species object on success, undef on failure Args : a classification string (eg 'Homo sapiens') and a NCBI taxon id (optional)
Objects are cached for parsing multiple sequence files.
_create_species
Title : _create_species Usage : Internal function Function: creates a Bio::Species object Returns : a Bio::Species object on success, undef on failure Args : a classification string (eg 'Homo sapiens') and a NCBI taxon id (optional)
_assign_identifier
Title : _assign_identifier Usage : Internal function Function: looks for sequence accession Returns : 1 on success Args : NONE
NCBI puts refseq accessions in TSeq_sid, others in TSeq_accver.
_convert_seqtype
Title : _convert_seqtype Usage : Internal function Function: maps Bio::Seq::alphabet() values [dna/rna/protein] onto TSeq_seqtype values [protein/nucleotide]
_get_idstring
Title : _get_idstring Usage : Internal function Function: parse accession and version info from TSeq_accver or TSeq_sid
_get_writer
Title : _get_writer Usage : Internal function Function: instantiate XML::Writer object if needed, output initial XML
close_writer
Title : close_writer Usage : $self->close_writer() Function: terminate XML output Args : NONE Returns : 1 on success
Called automatically by DESTROY when object goes out of scope