UNKNOWN

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

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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

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Index

NAME

SYNOPSIS

DESCRIPTION

OPTIONS

EXAMPLES

BUGS

AUTHOR

SEE ALSO

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