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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 Swissprot flat file databases.

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

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
 
 

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:

   http://bugzilla.open-bio.org/
 
 

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)