bp_chaos_plot(1p) [debian man page]

BP_CHAOS_PLOT(1p)					User Contributed Perl Documentation					 BP_CHAOS_PLOT(1p)

NAME

       chaos_plot - a chaos plot from DNA and RNA sequences

SYNOPSIS

	 chaos_plot.pl -i/--input=INPUTFILE -f/--format=SEQFORMAT
	       -o/--output=OUTPUTFILE -g/--graphics=GRAPHIC FORMAT
	       -w/--width=WIGHT -h/--height=HEIGHT

DESCRIPTION

       This scripts generates image files using GD image library to visualize nucleotide sequences using chaos plot.

OPTIONS

       Valid graphics formats are currently gd, gd2, png, wbmp, jpeg and gif.

       The default size of the image file is 600x400.

       The sequence input can be provided using any of the three methods:

       unnamed argument
	    chaos_plot filename

       named argument
	    chaos_plot -i filename

       standard input
	    chaos_plot < filename

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:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

HISTORY

       This code is based on EMBOSS C code for chaos.c by Ian Longden.	Included are documentation from EMBOSS code:

       Chaos produces a chaos plot.  The original application is part of the ACEDB genome database package, written by ** Richard Durbin (MRC LMB,
       UK) rd@mrc-lmba.cam.ac.uk, and Jean Thierry-Mieg (CRBM du CNRS, France) mieg@crbm1.cnusc.fr

perl v5.14.2							    2012-03-02							 BP_CHAOS_PLOT(1p)

Bio::SeqIO::chaosxml(3pm)				User Contributed Perl Documentation				 Bio::SeqIO::chaosxml(3pm)

NAME

       Bio::SeqIO::chaosxml - chaosxml sequence input/output stream

SYNOPSIS

	   #In general you will not want to use this module directly;
	   #use the chaosxml format via SeqIO

	   $outstream = Bio::SeqIO->new(-file => $filename, -format => 'chaosxml');

	   while ( my $seq = $instream->next_seq() ) {
	      $outstream->write_seq($seq);
	   }

DESCRIPTION

       This object can transform Bio::Seq objects to and from chaos files.

       CURRENTLY WRITE ONLY

       ChaosXML is an XML mapping of the chado relational database; for more information, see http://www.fruitfly.org/chaos-xml

       Chaos can have other syntaxes than XML (eg S-Expressions, Indented text)

       See Bio::SeqIO::chaos for a full description

VERY VERY IMPORTANT

       !!!!!!!!!!!CHADO AND CHAOS USE INTERBASE COORDINATES!!!!!!!!!!!!!!!!

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 one
       of 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:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Chris Mungall
       Email cjm@fruitfly.org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

perl v5.14.2							    2012-03-02						 Bio::SeqIO::chaosxml(3pm)