NAME

Bio::Assembly::IO - Handler for Assembly::IO Formats

SYNOPSIS

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);
}

DESCRIPTION

Bio::Assembly::IO is a handler module for formats in the Assembly::IO set (e.g. Bio::Assembly::IO::phrap).

FEEDBACK

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/

AUTHOR

Robson Francisco de Souza

E-mail: rfsouza@citri.iq.usp.br

CONTRIBUTORS

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APPENDIX

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.