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UNKNOWN

Section: User Commands (1)
Updated: September 2000
Index Return to Main Contents

 

NAME

unknown - indicate non-standard symbols in RNA, DNA and protein.

 

SYNOPSIS

unknown
[-e | --extended] [-c | --color | -Ccolor_r,color_g,color_b | --color=color_r,color_g,color_b] [-f | --fgcolor | -Fcolor_r,color_g,color_b | --fgcolor=color_r,color_g,color_b] [file]

 

DESCRIPTION

unknown adds/modifies color columns to color non-standard symbols (default is green). Input is either from file or stdin. The output is sent to stdout.

 

OPTIONS

unknown accepts the following options. No options are treated as -c.

-e
--extended
For nucleotides, the following extended alphabet is used: A, C, G, U, ..., B, D, H, V, N, X. For proteins, the following extensions to the alphabet is used: B, Z, X.

-c
--color
Color unknown symbols background green.

-f
--fgcolor
Color unknown symbols foreground green.

-Ccolor_r,color_g,color_b
--color=color_r,color_g,color_b
Specifies the rgb background color. color_x are numbers between 0 and 1, setting the relevant color part.

-Fcolor_r,color_g,color_b
--fgcolor=color_r,color_g,color_b
Specifies the rgb foreground color. color_x are numbers between 0 and 1, setting the relevant color part.

 

EXAMPLES

Color non-standard symbols red:

unknown -C1,0,0 foo.col

Only color symbols not in the extended set:

unknown -e foo.col

 

BUGS

Report bugs to col-bugs@bioinf.au.dk.

 

AUTHOR

Bjarne Knudsen (bk@daimi.au.dk)

 

SEE ALSO


 

Index

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLES
BUGS
AUTHOR
SEE ALSO


Comments, questions, etc., email gorodkin@genome.ku.dk.


Last updated March 26th, 2007 by Jan Gorodkin