Bio::SeqIO::tinyseq.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.bioperl.org
 
 

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