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.\" ========================================================================
.\"
.IX Title "BP_CHAOS_PLOT 1p"
.TH BP_CHAOS_PLOT 1p "2019-11-28" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
bp_chaos_plot \- a chaos plot from DNA and RNA sequences
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&  bp_chaos_plot.pl \-i/\-\-input=INPUTFILE \-f/\-\-format=SEQFORMAT
\&        \-o/\-\-output=OUTPUTFILE \-g/\-\-graphics=GRAPHIC FORMAT
\&        \-w/\-\-width=WIGHT \-h/\-\-height=HEIGHT
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This scripts generates image files using \s-1GD\s0 image library to visualize
nucleotide sequences using chaos plot.
.SH "OPTIONS"
.IX Header "OPTIONS"
Valid graphics formats are currently gd, gd2, png, wbmp, jpeg and gif.
.PP
The default size of the image file is 600x400.
.PP
The sequence input can be provided using any of the three methods:
.IP "unnamed argument" 3
.IX Item "unnamed argument"
.Vb 1
\&  bp_chaos_plot filename
.Ve
.IP "named argument" 3
.IX Item "named argument"
.Vb 1
\&  bp_chaos_plot \-i filename
.Ve
.IP "standard input" 3
.IX Item "standard input"
.Vb 1
\&  bp_chaos_plot < filename
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason@bioperl.org
.SH "HISTORY"
.IX Header "HISTORY"
This code is based on \s-1EMBOSS C\s0 code for chaos.c by Ian Longden.
Included are documentation from \s-1EMBOSS\s0 code:
.PP
Chaos produces a chaos plot.  The original application is part of the
\&\s-1ACEDB\s0 genome database package, written by ** Richard Durbin (\s-1MRC LMB,
UK\s0) rd@mrc\-lmba.cam.ac.uk, and Jean Thierry-Mieg (\s-1CRBM\s0 du \s-1CNRS,\s0
France) mieg@crbm1.cnusc.fr