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://redmine.open-bio.org/projects/bioperl/

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