Bio::SeqIO::swiss(3pm)					User Contributed Perl Documentation				    Bio::SeqIO::swiss(3pm)

NAME

       Bio::SeqIO::swiss - Swissprot sequence input/output stream

SYNOPSIS

       It is probably best not to use this object directly, but rather go through the SeqIO handler system:

	   use Bio::SeqIO;

	   $stream = Bio::SeqIO->new(-file => $filename,
				     -format => 'swiss');

	   while ( my $seq = $stream->next_seq() ) {
	      # do something with $seq
	   }

DESCRIPTION

       This object can transform Bio::Seq objects to and from Swiss-Pprot flat file databases.

       There is a lot of flexibility here about how to dump things which needs to be documented.

   GN (Gene name) line management details
       A Uniprot/Swiss-Prot entry holds information on one protein sequence. If that sequence is identical across genes and species, they are all
       merged into one entry. This creates complex needs for several annotation fields in swiss-prot format.

       The latest syntax for GN line is described in the user manual:

	 http://www.expasy.ch/sprot/userman.html#GN_line

       Each of the possibly multiple genes in an entry can have Name, Synonyms (only if there is a name), OrderedLocusNames (names from genomic
       sequences) and ORFNames (temporary or cosmid names). "Name" here really means "symbol". This complexity is now dealt with the following
       way:

       A new Bio::AnnotationI class was created in order to store the data in tag-value pairs.	This class (Bio::Annotation::TagTree) is stored in
       the Bio::Annotation::Collection object and is accessed like all other annotations. The tag name is 'gene_name'.

       There is a single Bio::Annotation::TagTree per sequence record, which corresponds to the original class that stored this data
       (Bio::Annotation::StructuredValue).  Depending on how we progress this may change to represent each group of gene names.

       For now, to access the gene name tree annotation, one uses the below method:

	  my ($gene) = $seq->annotation->get_Annotations('gene_name');

       If you are only interested in displaying the values, value() returns a string with similar formatting.

       There are several ways to get directly at the information you want if you know the element (tag) for the data.  For gene names all data is
       stored with the element-tag pairs:

	 "element1=tag1, tag2, tag3; element2=tag4, tag5;"

       This normally means the element will be 'Name', 'Synonyms', etc. and the gene names the values.	Using findval(), you can do the following:

	 # grab a flattened list of all gene names
	 my @names = $ann->findval('Name');

	 # or iterated through the nodes and grab the name for each group
	 for my $node ($ann->findnode('gene_name')) {
	    my @names = $node->findval('Name');
	 }

       The current method for parsing gene name data (and reconstructing gene name output) is very generic. This is somewhat preemptive if, for
       instance, UniProt decides to update and add another element name to the current ones using the same formatting layout. Under those
       circumstances, one can iterate through the tag tree in a safe way and retrieve all node data like so.

	 # retrieve the gene name nodes (groups like names, synonyms, etc).
	 for my $ann ($seq->annotation->get_Annotations('gene_name')) {

	     # each gene name group
	     for my $node ($ann->findnode('gene_name')) {
		 print "Gene name:
";

		 # each gene name node (tag => value pair)
		 for my $n ($node->children) {
		     print "	".$n->element.": ".$n->children."
";
		 }
	     }
	 }

       For more uses see Bio::Annotation::TagTree.

       Since Uniprot/Swiss-Prot format have been around for quite some time, the parser is also able to read in the older GN line syntax where
       genes are separated by AND and various symbols by OR. The first symbol is taken to be the 'Name' and the remaining ones are stored as
       'Synonyms'.

       Also, for UniProt output we support using other Bio::AnnotationI, but in this case we only use the stringified version of the annotation.
       This is to allow for backwards compatibility with code that previously used Bio::Annotation::SimpleValue or other Bio::AnnotationI classes.

   Optional functions
       _show_dna()
	  (output only) shows the dna or not

       _post_sort()
	  (output only) provides a sorting func which is applied to the FTHelpers before printing

       _id_generation_func()
	  This is function which is called as

	     print "ID	 ", $func($seq), "
";

	  To generate the ID line. If it is not there, it generates a sensible ID line using a number of tools.

	  If you want to output annotations in Swissprot format they need to be stored in a Bio::Annotation::Collection object which is accessible
	  through the Bio::SeqI interface method annotation().

	  The following are the names of the keys which are polled from a Bio::Annotation::Collection object.

	   reference   - Should contain Bio::Annotation::Reference objects
	   comment     - Should contain Bio::Annotation::Comment objects
	   dblink      - Should contain Bio::Annotation::DBLink objects
	   gene_name   - Should contain Bio::Annotation::SimpleValue object

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 one
       of the Bioperl mailing lists.  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 the bugs and their resolution.  Bug reports can be submitted via the
       web:

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

AUTHOR - Elia Stupka
       Email elia@tll.org.sg

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	:

   write_seq
	Title	: write_seq
	Usage	: $stream->write_seq($seq)
	Function: writes the $seq object (must be seq) to the stream
	Returns : 1 for success and 0 for error
	Args	: array of 1 to n Bio::SeqI objects

   _generateCRCTable
	Title	: _generateCRCTable
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   _crc32
	Title	: _crc32
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   _crc64
	Title	: _crc64
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   _print_swissprot_FTHelper
	Title	: _print_swissprot_FTHelper
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   _read_swissprot_References
	Title	: _read_swissprot_References
	Usage	:
	Function: Reads references from swissprot format. Internal function really
	Example :
	Returns :
	Args	:

   _read_swissprot_Species
	Title	: _read_swissprot_Species
	Usage	:
	Function: Reads the swissprot Organism species and classification
		  lines.
		    Able to deal with unconventional species names.
	Example : OS Unknown prokaryotic organism
		    $genus = undef ; $species = Unknown prokaryotic organism
	Returns : A Bio::Species object
	Args	:

   _filehandle
	Title	: _filehandle
	Usage	: $obj->_filehandle($newval)
	Function:
	Example :
	Returns : value of _filehandle
	Args	: newvalue (optional)

   _read_FTHelper_swissprot
	Title	: _read_FTHelper_swissprot
	Usage	: _read_FTHelper_swissprot($buffer)
	Function: reads the next FT key line
	Example :
	Returns : Bio::SeqIO::FTHelper object
	Args	:

   _write_line_swissprot
	Title	: _write_line_swissprot
	Usage	:
	Function: internal function
	Example :
	Returns :
	Args	:

   _write_line_swissprot_regex
	Title	: _write_line_swissprot_regex
	Usage	:
	Function: internal function for writing lines of specified
		  length, with different first and the next line
		  left hand headers and split at specific points in the
		  text
	Example :
	Returns : nothing
	Args	: file handle, first header, second header, text-line, regex for line breaks, total line length

   _post_sort
	Title	: _post_sort
	Usage	: $obj->_post_sort($newval)
	Function:
	Returns : value of _post_sort
	Args	: newvalue (optional)

   _show_dna
	Title	: _show_dna
	Usage	: $obj->_show_dna($newval)
	Function:
	Returns : value of _show_dna
	Args	: newvalue (optional)

   _id_generation_func
	Title	: _id_generation_func
	Usage	: $obj->_id_generation_func($newval)
	Function:
	Returns : value of _id_generation_func
	Args	: newvalue (optional)

   _ac_generation_func
	Title	: _ac_generation_func
	Usage	: $obj->_ac_generation_func($newval)
	Function:
	Returns : value of _ac_generation_func
	Args	: newvalue (optional)

   _sv_generation_func
	Title	: _sv_generation_func
	Usage	: $obj->_sv_generation_func($newval)
	Function:
	Returns : value of _sv_generation_func
	Args	: newvalue (optional)

   _kw_generation_func
	Title	: _kw_generation_func
	Usage	: $obj->_kw_generation_func($newval)
	Function:
	Returns : value of _kw_generation_func
	Args	: newvalue (optional)

perl v5.14.2							    2012-03-02						    Bio::SeqIO::swiss(3pm)