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.
(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
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args :
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
Title : _generateCRCTable Usage : Function: Example : Returns : Args :
Title : _crc32 Usage : Function: Example : Returns : Args :
Title : _crc64 Usage : Function: Example : Returns : Args :
Title : _print_swissprot_FTHelper Usage : Function: Example : Returns : Args :
Title : _read_swissprot_References Usage : Function: Reads references from swissprot format. Internal function really Example : Returns : Args :
Title : _read_swissprot_Species Usage : Function: Reads the swissprot Organism species and classification lines. Example : Returns : A Bio::Species object Args :
Title : _filehandle Usage : $obj->_filehandle($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional)
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
Title : _write_line_swissprot Usage : Function: internal function Example : Returns : Args :
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
Title : _post_sort Usage : $obj->_post_sort($newval) Function: Returns : value of _post_sort Args : newvalue (optional)
Title : _show_dna Usage : $obj->_show_dna($newval) Function: Returns : value of _show_dna Args : newvalue (optional)
Title : _id_generation_func Usage : $obj->_id_generation_func($newval) Function: Returns : value of _id_generation_func Args : newvalue (optional)
Title : _ac_generation_func Usage : $obj->_ac_generation_func($newval) Function: Returns : value of _ac_generation_func Args : newvalue (optional)
Title : _sv_generation_func Usage : $obj->_sv_generation_func($newval) Function: Returns : value of _sv_generation_func Args : newvalue (optional)
Title : _kw_generation_func Usage : $obj->_kw_generation_func($newval) Function: Returns : value of _kw_generation_func Args : newvalue (optional)
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.