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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 [email protected]

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)