NAME¶
Bio::SeqIO::tinyseq - reading/writing sequences in NCBI TinySeq format
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.
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>
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