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STDPAIR

Section: User Commands (1)
Updated: September 2000
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NAME

stdpair - remove/indicate non-standard base-pairs in RNA

 

SYNOPSIS

stdpair
[-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

stdpair removes base pairs in RNA that are not A-U, C-G, or G-U. Input is either from file or stdin. The output is sent to stdout.

stdpair can also be used to add/modify color columns to color nucleotides participating in non-standard base-pairs.

 

OPTIONS

stdpair accepts the following options.

-c
--color
Color nucleotides background (red) instead of changing the structure.

-f
--fgcolor
Color nucleotide foreground (red) instead of changing the structure.

-Ccolor_r,color_g,color_b
--color=color_r,color_g,color_b
Like -c except that the rgb color is specified. 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
Like -f except that the rgb color is specified. color_x are numbers between 0 and 1, setting the relevant color part.

 

EXAMPLES

Remove non-standard base-pairs in file foo.col:

stdpair foo.col

Color non-standard base-pairs red:

stdpair -c foo.col

Color non-standard base-pairs green:

stdpair -C0,1,0 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