/ 
BioPerl-1.007001
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Assembly::IO

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:

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

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   : $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
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