Bio::Assembly::IO(3pm) User Contributed Perl Documentation 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:
https://redmine.open-bio.org/projects/bioperl/
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
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
perl v5.14.2 2012-03-02 Bio::Assembly::IO(3pm)