COL2TXTALIGN
Section: User Commands (1) Updated: September 2000 Index
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NAME
col2txtalign - Make text alignment from col file
SYNOPSIS
- col2txtalign
-
[-rrange
| -range=range]
[--namewidth=namewidth]
[--textwidth=textwidth]
[--space]
[file]
DESCRIPTION
col2txtalign
creates a text output that shows the sequences in the input file. It
is assumed that the input file contains aligned sequences, such that
they are equal in length (including gaps).
Input is either from
file
or stdin. The output is sent to stdout.
OPTIONS
col2txtalign
accepts the following options.
- -rrange
-
- --range=range
-
Only prints the positions defined by
range.
The range is specified as position intervals seperated by commas, like
`-r1-20,50-100,139'
which makes
col2txtalign
output positions 1-20, 50-100, and 139.
- --space
-
Inserts spaces for every ten positions.
--textwidth
option is used, in which case it fits
textwidth
characters of the alignment to the page width.
- --namewidth=namewidth
-
Sets the width of the sequnece names to
namewidth.
The units of
namewidth
is the fontsize. The default value is 8. This means that the sequence
name width is 64 points (since the default font size is 8).
- --textwidth=textwidth
-
Sets the width of the sequence field to
textwidth.
The units of
textwidth
is characters. Notice that a space is inserted for each 10
positions. These spaces are also counted. This means that
textwidth
should be 54 if 50 positions should be displayed in every line (since
4 spaces are inserted).
EXAMPLES
Make a text alignment:
-
col2txtalign foo.col
Make a text output with spaces for every ten positions, 20 sequence
positions on each line (notice the 21 because of the space character
between blocks of 10 positions). Only five characters of the name are
shown:
-
col2txtalign --space --namewidth=5 --textwidth=21 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.
|
