Bio::SeqIO::GenBank - GenBank 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 => 'GenBank'); while ( my $seq = $stream->next_seq() ) { # do something with $seq }
This object can transform Bio::Seq objects to and from GenBank flat file databases.
There is alot 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.
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Email elia@ebi.ac.uk
Ewan Birney birney@ebi.ac.uk Jason Stajich jason@bioperl.org Chris Mungall cjm@fruitfly.bdgp.berkeley.edu Lincoln Stein lstein@cshl.org Heikki Lehvaslaiho, heikki@ebi.ac.uk
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 $seq object (must be seq) to the stream Returns : 1 for success and 0 for error Args : Bio::Seq
Title : _print_GenBank_FTHelper Usage : Function: Example : Returns : Args :
Title : _read_GenBank_References Usage : Function: Reads references from GenBank format. Internal function really Example : Returns : Args :
Title : _read_GenBank_Species Usage : Function: Reads the GenBank Organism species and classification lines. Example : Returns : A Bio::Species object Args :
Title : _read_FTHelper_GenBank Usage : _read_FTHelper_GenBank($buffer) Function: reads the next FT key line Example : Returns : Bio::SeqIO::FTHelper object Args : filehandle and reference to a scalar
Title : _write_line_GenBank Usage : Function: internal function Example : Returns : Args :
Title : _write_line_GenBank_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.