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Full Discussion: Help in awk/bash
Top Forums Shell Programming and Scripting Help in awk/bash Post 302752131 by bioinfo on Saturday 5th of January 2013 05:38:56 PM
Old 01-05-2013
Quote:
You said you had two two files: atom.txt and g.txt. I am assuming that atom.txt is in the same format as 11.txt in your last thread with the same title as this thread.
Yes, atom.txt is same as 11.txt. While posting in new thread I just used new name Smilie . I am explaining my problem again with more details and concise data. I have two files atom.txt (or 11.txt from other thread) and g.txt (which I made using data from raw files file 1 and file 2). If you feel that it will be easy to retreive data directly from file 1 and file 2 rather that using g.txt for retreiving patterns from atom.txt, I will be happy to go for it too.

g.txt (made it more concise and short; in reality I have 10 groups for this file out of more than 600 groups from file 1. Based on decreasing number of branches they are grouped into 10 groups in g.txt but I am showing only 2 here)
Code:
Group   Centre      Branches       Id_of_Branches
 3       006          6         009,004,008,007,005,006
 5       012          2         012,013

file 1:
Code:
Group: 0 Number of Branches: 1
0    001
Centre: 001 Branches: 1
Group: 1 Number of Branches: 1
0    002
Centre: 002 Branches: 1
Group: 2 Number of Branches: 1
0    003
Centre: 003 Branches: 1
Group: 3 Number of Branches: 6
0    009
1    004
2    008
3    007
4    005
5    006
Centre: 006 Branches: 6
Group: 4 Number of Branches: 2
0    010
1    011
Centre: 010 Branches: 2
Group: 5 Number of Branches: 2
0    012
1    013
Centre: 012 Branches: 2
Upto more than 600 groups

file2:
Code:
Group No:
 3        Centre: 006 Branches: 6                   
 5        Centre: 012 Branches: 2

Required output:
Corresponding to value of Id_of_Branches from g.txt, I wish to retreive that pattern from atom.txt.
Therefore, in this sample data, I required 3 output files; 2 files corresponding to all IDs from 2 groups and 3rd file for patterns corresponding to Id of Centre from all groups:

Code:
(1) g3.txt
#009
ATOM 1 N SER A 1 35.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 35.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL
#004
ATOM 1 N SER A 1 34.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 35.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL
#008
ATOM 1 N SER A 1 45.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 35.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL
#007
ATOM 1 N SER A 1 50.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 65.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL
#005
ATOM 1 N SER A 1 90.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 89.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL
#006
ATOM 1 N SER A 1 67.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 23.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL

(2)g5.txt
#012
ATOM 1 N SER A 1 37.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 37.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL
#13
ATOM 1 N SER A 1 40.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 31.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL

(3) Centre.txt (For Id from centre of all groups)
#006
ATOM 1 N SER A 1 67.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 23.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL
#012
ATOM 1 N SER A 1 37.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 37.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL

Hope I am able to make my problem more clear. Smilie
 

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