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:\n";

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

       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), "\n";

          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://github.com/bioperl/bioperl-live/issues

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)