NAME

Bio::Tools::Run::PiseApplication::extractfeat

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::extractfeat

      Bioperl class for:

        EXTRACTFEAT     Extract features from a sequence (EMBOSS)


      Parameters: 

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


                extractfeat (String)

                init (String)

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

                before (Integer)
                        Amount of sequence before feature to extract (-before)

                after (Integer)
                        Amount of sequence after feature to extract (-after)

                source (String)
                        Source of feature to display (-source)

                type (String)
                        Type of feature to extract (-type)

                sense (Integer)
                        Sense of feature to extract (-sense)

                minscore (Float)
                        Minimum score of feature to extract (-minscore)

                maxscore (Float)
                        Maximum score of feature to extract (-maxscore)

                tag (String)
                        Tag of feature to extract (-tag)

                value (String)
                        Value of feature tags to extract (-value)

                join (Switch)
                        Output introns etc. as one sequence (-join)

                featinname (Switch)
                        Append type of feature to output sequence name (-featinname)

                outseq (OutFile)
                        outseq (-outseq)
                        pipe: seqfile

                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/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/extractfeat.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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