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BioPerl-1.7.7
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SeqIO::tinyseq

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