bp_chaos_plot − a chaos plot from DNA and RNA sequences
bp_chaos_plot.pl −i/−−input=INPUTFILE −f/−−format=SEQFORMAT −o/−−output=OUTPUTFILE −g/−−graphics=GRAPHIC FORMAT −w/−−width=WIGHT −h/−−height=HEIGHT
This scripts generates image files using GD image library to visualize nucleotide sequences using chaos plot.
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
bp_chaos_plot filename
named argument
bp_chaos_plot −i filename
standard input
bp_chaos_plot < filename
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 AT bioperl DOT 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://github.com/bioperl/bioperl−live/issues
Email jason AT bioperl DOT org
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 AT crbm1 DOT cnusc DOT fr