Bio::Assembly::IO - Handler for Assembly::IO Formats
use Bio::Assembly::IO;
$in = Bio::Assembly::IO->new(-file=>"<inputfilename",
-format=>'phrap');
$out = Bio::Assembly::IO->new(-file=>">outputfilename",
-format=>'phrap');
while ( my $seq = $in->next_seq() ) {
$out->write_seq($seq);
}
Bio::Assembly::IO is a handler module for formats in the Assembly::IO set (e.g. Bio::Assembly::IO::phrap).
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to 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
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/
Robson Francisco de Souza
E-mail: rfsouza@citri.iq.usp.br
#
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : Bio::Assembly::IO->new(-file =>$filename,-format=>'format')
Function: Returns a new assembly stream
Returns : A Bio::Assembly::IO::Handler initialised
with the appropriate format
Args : -file => $filename
-format => format
Title : next_assembly Usage : $cluster = $stream->next_assembly() Function: Reads the next assembly object from the stream and returns it. Returns : a Bio::Assembly::ScaffoldI compliant object Args : none
Title : _load_format_module Usage : *INTERNAL Assembly::IO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args :
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function: guess format based on file suffix
Example :
Returns : guessed format of filename (lower case)
Args :
Notes : formats that _filehandle() will guess includes
only phrap, by now.
