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TXT2COL

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

txt2col - convert text format to col format.  

SYNOPSIS

txt2col
[-m | --mask] [file]
 

DESCRIPTION

txt2col converts text format to col format. The text format looks like this:


  pairing_mask ---3--3111-------111--
  XXXXXXXXXX   -gcAugUcuggauc--ccgug-
  orgb         agcAcgUcg-Gauca-Ccgug-
  orgc         cgcAacUcuggauc--acggu-
  orgd         -gcAchUgcggauc-uacgug-

First the name, then the sequence. Note that the first sequence has to have the name `pairing_mask'. Theis sequence specifies RNA structure.

 

OPTIONS

txt2col accepts the following option.

-m
--mask
Output pairing mask as first entry.
 

EXAMPLES

Convert text file to col file with pairing mask as first entry.

txt2col -m foo.txt

 

BUGS

The program should work for other sequences than RNA and without the pairing mask.

Report opther 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