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Bio::Assembly::IO.3pm
Langue: en
Version: 2010-05-19 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Assembly::IO - Handler for Assembly::IO FormatsSYNOPSIS
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; $out->close;
DESCRIPTION
Bio::Assembly::IO is a handler module for formats in the Assembly::IO set (e.g. Bio::Assembly::IO::phrap).FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated.bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:http://bugzilla.open-bio.org/
AUTHOR
Robson Francisco de SouzaE-mail: rfsouza@citri.iq.usp.br
CONTRIBUTORS
#APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
Title : new Usage : Bio::Assembly::IO->new(-file =>$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.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre