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).

Mailing Lists
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

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/ 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 _

new
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

next_assembly
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

_load_format_module
Title : _load_format_module Usage : *INTERNAL Assembly::IO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args :

_guess_format
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.