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

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