Reference

Bio::Assembly::IO(3pm)

Handler for Assembly::IO Formats

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR

Robson Francisco de Souza

E-mail: [email protected]

CONTRIBUTORS

#

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : $stream = 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

format

 Title   : format
 Usage   : $format = $stream->format()
 Function: Get the assembly format
 Returns : assembly format
 Args    : none

next_assembly

 Title   : next_assembly
 Usage   : $scaffold = $stream->next_assembly()
 Function: Reads the next assembly object from the stream and returns it.
 Returns : a Bio::Assembly::ScaffoldI compliant object
 Args    : none

next_contig

 Title   : next_contig
 Usage   : $contig = $stream->next_contig()
 Function: Reads the next contig or singlet from the stream and returns it.
 Returns : a Bio::Assembly::Contig or Bio::Contig::Assembly::Singlet
 Args    : none

write_assembly

  Title   : write_assembly
  Usage   : $stream->write_assembly($assembly)
  Function: Write the assembly object in desired format. This method calls
            write_header(), write_contigs() and write_footer() internally.
  Returns : 1 on success, 0 for error
  Args    : A Bio::Assembly::Scaffold object

write_header

  Title   : write_header
  Usage   : $stream->write_header($assembly)
  Function: Write the start of the assembly file. It can be called at any time,
            not when starting to write the assembly file. 
  Returns : 1 on success, 0 for error
  Args    : A Bio::Assembly::Scaffold object or ... (check the specific format
            driver for more details)

write_contig

  Title   : write_contig
  Usage   : $stream->write_contig($contig)
  Function: Write a contig object in the desired format.
  Returns : 1 on success, 0 for error
  Args    : A Bio::Assembly::Contig object

write_footer

  Title   : write_footer
  Usage   : $stream->write_footer($assembly)
  Function: Write the start of the assembly file.
  Returns : 1 on success, 0 for error
  Args    : A Bio::Assembly::Scaffold object or ... (check the specific format
            driver for more details)

_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
           ace, phrap and tigr at the moment

_sort

    Title   : _sort
    Usage   : @sorted_values = $ass_io->_sort(@values)
    Function: Sort a list of values naturally if Sort::Naturally is installed
              (nicer), lexically otherwise (not as nice, but safe)
    Returns : array of sorted values
    Args    : array of values to sort

History