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COL2TXTALIGN

Section: User Commands (1)
Updated: September 2000
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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@genome.ku.dk.


Last updated March 26th, 2007 by Jan Gorodkin