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UNKNOWN
Section: User Commands (1) Updated: September 2000 Index
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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
Index
- NAME
-
- SYNOPSIS
-
- DESCRIPTION
-
- OPTIONS
-
- EXAMPLES
-
- BUGS
-
- AUTHOR
-
- SEE ALSO
-
Comments, questions, etc., email
gorodkin@rth.dk.
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Last updated March 26th, 2007 by Jan Gorodkin
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