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Bio::Tools::Run::PiseApplication::checktrans.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::checktransSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::checktransBioperl class for: CHECKTRANS Reports STOP codons and ORF statistics of a protein (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/checktrans.html for available values): checktrans (String) init (String) sequence (Sequence) sequence -- stopprotein [sequences] (-sequence) pipe: seqsfile orfml (Integer) Minimum ORF Length to report (-orfml) report (OutFile) report (-report) outseq (OutFile) Sequence file to hold output ORF sequences (-outseq) pipe: seqsfile outseq_sformat (Excl) Output format for: Sequence file to hold output ORF sequences featout (OutFile) Feature file for output (-featout) featout_offormat (Excl) Feature output format (-offormat) addlast (Switch) Force the sequence to end with an asterisk (-addlast) auto (String)
FEEDBACK
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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:http://bugzilla.open-bio.org/
AUTHOR
Catherine Letondal (letondal@pasteur.fr)COPYRIGHT
Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
DISCLAIMER
This software is provided ``as is'' without warranty of any kind.SEE ALSO
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- http://bioweb.pasteur.fr/seqanal/interfaces/checktrans.html
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- Bio::Tools::Run::PiseApplication
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- Bio::Tools::Run::AnalysisFactory::Pise
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- Bio::Tools::Run::PiseJob
new
Title : new() Usage : my $checktrans = Bio::Tools::Run::PiseApplication::checktrans->new($location, $email, @params); Function: Creates a Bio::Tools::Run::PiseApplication::checktrans object. This method should not be used directly, but rather by a Bio::Tools::Run::AnalysisFactory::Pise instance. my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new(); my $checktrans = $factory->program('checktrans'); Example : - Returns : An instance of Bio::Tools::Run::PiseApplication::checktrans.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre