| Bio::Assembly::IO(3pm) | User Contributed Perl Documentation | Bio::Assembly::IO(3pm) |
Bio::Assembly::IO - Handler for Assembly::IO Formats
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;
Bio::Assembly::IO is a handler module for formats in the Assembly::IO set (e.g. Bio::Assembly::IO::phrap).
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
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.
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
Robson Francisco de Souza
E-mail: rfsouza@citri.iq.usp.br
#
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : format Usage : $format = $stream->format() Function: Get the assembly format Returns : assembly format Args : none
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
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
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
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)
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)
Title : _load_format_module Usage : *INTERNAL Assembly::IO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args :
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
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
| 2018-10-27 | perl v5.26.2 |