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Bio::Assembly::IO.3pm

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 $scaffold = $in->next_assembly() ) {
        # do something with Bio::Assembly::Scaffold instance
        # ...
        $out->write_assembly(-scaffold => $scaffold);
     }
 
     $in->close;
     $out->close;
 
 

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://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR

Robson Francisco de Souza

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

CONTRIBUTORS

#

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
 
 

write_assembly

   Title   : write_assembly
   Usage   : $ass_io->write_assembly($assembly)
   Function: Write the assembly object in Phrap compatible ACE format
   Returns : 1 on success, 0 for error
   Args    : A Bio::Assembly::Scaffold object
 
 

_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.