NAME

Bio::Tools::Run::PiseApplication::trimseq

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::trimseq

      Bioperl class for:

	TRIMSEQ	Trim ambiguous bits off the ends of sequences (EMBOSS)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/trimseq.html 
         for available values):


		trimseq (String)

		init (String)

		sequence (Sequence)
			sequence -- gapany [sequences] (-sequence)
			pipe: seqsfile

		window (Integer)
			Window size (-window)

		percent (Float)
			Percent threshold of ambiguity in window (-percent)

		strict (Switch)
			Trim off all ambiguity codes, not just N or X (-strict)

		star (Switch)
			Trim off asterisks (-star)

		left (Switch)
			Trim at the start (-left)

		right (Switch)
			Trim at the end (-right)

		outseq (OutFile)
			outseq (-outseq)
			pipe: seqsfile

		outseq_sformat (Excl)
			Output format for: outseq

		auto (String)

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/wiki/Mailing_lists  - 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 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

• http://bioweb.pasteur.fr/seqanal/interfaces/trimseq.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

Title   : new()
Usage   : my $trimseq = Bio::Tools::Run::PiseApplication::trimseq->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::trimseq 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 $trimseq = $factory->program('trimseq');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::trimseq.