Bio::SeqIO::swiss - Swissprot sequence input/output stream It is probably best not to use this object directly, but rather go through the SeqIO handler system. Go: $stream = Bio::SeqIO->new(-file => $filename, -format => 'swiss'); while ( my $seq = $stream->next_seq() ) { # do something with $seq } 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 I need to document fully.

Optional functions
(output only) shows the dna or not (output only) provides a sorting func which is applied to the FTHelpers before printing 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

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://bio.perl.org/MailList.html - 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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email elia@tll.org.sg Describe contact details here 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. Example : 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 : filehandle and reference to a scalar

_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)