NAME
Bio::Tools::Run::PiseApplication::sreformat
SYNOPSIS
#
DESCRIPTION
Bio::Tools::Run::PiseApplication::sreformat
Bioperl class for:
HMMER sreformat - convert sequence file to different format (S. Eddy)
Parameters:
(see also:
http://bioweb.pasteur.fr/seqanal/interfaces/sreformat.html
for available values):
sreformat (String)
seqfile (InFile)
Sequence(s) file
pipe: hmmer_alig
output_format (Excl)
output format
dna (Switch)
DNA (-d)
lowercase (Switch)
Convert all sequence residues to lower case (-l)
rna (Switch)
RNA (-r)
uppercase (Switch)
Convert all sequence residues to upper case (-u)
iupac_convert (Switch)
Convert DNA non-IUPAC characters (such as X's) to N's (-x)
pfam (Switch)
(--pfam)
sam (Switch)
(--sam)
samfrac (Float)
(--samfrac x)
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 list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
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 email or the web:
bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/
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
http://bioweb.pasteur.fr/seqanal/interfaces/sreformat.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob
new
Title : new()
Usage : my $sreformat = Bio::Tools::Run::PiseApplication::sreformat->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::sreformat 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 $sreformat = $factory->program('sreformat');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::sreformat.