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Bio::SeqIO::tinyseq(3)User Contributed Perl DocumentatioBio::SeqIO::tinyseq(3)

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 <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>

       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

perl v5.32.0			  2019-12-07		Bio::SeqIO::tinyseq(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | SEE ALSO | AUTHOR | APPENDIX

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