Reformatting a file for biological purpose Post: 302791211

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Top Forums Shell Programming and Scripting Reformatting a file for biological purpose Post 302791211 by paolo.kunder on Monday 8th of April 2013 06:36:15 AM

04-08-2013

Registered User

Reformatting a file for biological purpose

Dear ALL,
I would really appreciate if you could help me in reformatting a file in this way:

The file refers to a list of genetic coordinates, each lines has a score value and the associated chromosome is listed in the line starting with chrom .

If more coordinates are found, the start refers to the start plus n lines:

original file

Code:

chrom=chr1 start=3000306
0.006
0.010
0.014
chrom=chrX start=40000306
0.014
chrom=chr9 start=80000306 
0.1
0.2

I would like to obtain a file like this

Code:

#chr #start #end #score

chr1 3000306 3000307 0.006
chr1 3000307 3000308 0.010
chr1 3000308 3000309 0.019
chrX 40000306 40000307 0.014
chr9 80000306 80000307 0.1
chr9 80000307 80000308 0.2

Let me know if you can help me, the original file in up to 1 GB and is impossible editing my hand,
Thanks,
Paolo

Last edited by paolo.kunder; 04-08-2013 at 07:42 AM..

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LEARN ABOUT DEBIAN

tmscore

TMSCORE(1)						      General Commands Manual							TMSCORE(1)

NAME

       TM-score - an algorithm to calculate the similarity of topologies of two protein structures

VERSION

       This documentation refers to TM-score version released on 2011/01/30

SYNOPSIS

       1. Run TM-score to compare 'model' and 'native':

	   TMscore model native

       2. Run TM-score with an assigned d0, e.g. 5 Angstroms:

	   TMscore model native -d 5

       3. Run TM-score with superposition output, e.g. 'TM.sup', and view in Rasmol:

	   TMscore model native -o TM.sup
	   rasmol -script TM.sup

DESCRIPTION

       This program is to compare two protein structures and identify the best superposition that has the highest TM-score. Input structures must
       be in the PDB format. By default, TM-score is normalized by the second protein. Users can obtain a brief instruction by simply running the
       program without arguments.

OPTIONS

	   -o filename.sup Outputs the superposition to the specified file,
	      suitable for use in rasmol.

	   -d value Sets d0 to the specified number of angstroms.

SEE ALSO

       TMalign, rasmol

       When  using  this proram and for more detailed information, please refer to the publication in NucleicAcidsRes.	(2005) Volume 33 page
       2303ff. by Zhang and Skolnick.

AUTHOR

       For comments/suggestions,please contact email: zhng@umich.edu.

       This manpage was compiled by Tim Booth (tbooth@ceh.ac.uk)

.								    2011-02-03								TMSCORE(1)