Login or Register to Ask a Question and Join Our Community


UNIX for Dummies Questions & Answers

replace a column with values from another file

 
Thread Tools Search this Thread
Top Forums UNIX for Dummies Questions & Answers replace a column with values from another file
# 1  
Old 07-04-2011
replace a column with values from another file
Dear all,

I have a file1.pdb in pdb format and a dat file2 containing values, corresponding to the atoms in the pdb file. these values (file2.dat) need to be in the column instead of the 0.00 (file1) values for each atom in file1.pdb .(the red values must be replaced by the blue ones,in order)

Input:

file1.pdb
Code:
ATOM   1       C    PHE  1    48.343 23.545 32.02 1.00 0.00       C
ATOM   2       H    HIE   1    48.343 23.545 32.02 1.00 0.00      H
ATOM   3       C    PHE  1    48.343 23.545 32.02 1.00 0.00       C
ATOM   4       N    ALA  1    48.343 23.545 32.02 1.00 0.00       N
ATOM   5       0    VAL   1    48.343 23.545 32.02 1.00 0.00      O

file2.dat

Code:
20.568
98.346
17.837
14.469
57.537

OUTPUT:

file3.pdb
Code:
ATOM   1       C    PHE  1    48.343 23.545 32.02 1.00 20.568      C
ATOM   2       H    HIE   1    48.343 23.545 32.02 1.00 98.346      H
ATOM   3       C    PHE  1    48.343 23.545 32.02 1.00 17.837       C
ATOM   4       N    ALA  1    48.343 23.545 32.02 1.00 14.469       N
ATOM   5       0    VAL   1    48.343 23.545 32.02 1.00 57.537      O


Thanks,

Po
Last edited by Franklin52; 07-04-2011 at 05:39 AM.. Reason: Please use code tags for code and data samples, thank you
# 2  
Old 07-04-2011
Code:
awk 'NR==FNR{a[NR]=$0;next}{$10=a[FNR]}1' file2.dat file1.pdb

This User Gave Thanks to bartus11 For This Post:
# 3  
Old 07-04-2011
Thanks bartus11,
It works but does not retain the original format of the pdb file .
How can we do the same thing, without disturbing the format (pdb format) of the file1.pdb?
# 4  
Old 07-04-2011
Try:
Code:
perl -pe 'BEGIN{open I,"file2.dat";chomp(@x=<I>)};s/0.00(\s+\w)$/$x[$.-1]\1/' file1.pdb

# 5  
Old 07-04-2011
Assuming the value "0.00" occurs once in a record:
Code:
awk 'NR==FNR{a[NR]=$0; next}{sub("0.00",a[FNR])}1' file2.pdb file1.pdb

This User Gave Thanks to Franklin52 For This Post:
chen.xiao.po
# 6  
Old 07-04-2011
the above perl command was executed.

the format of the pdb was maintained, however, the output is identical to the original pdb input (file1.pdb). (i.e. the red values remained as it is and were not replaced by the blue ones)

---------- Post updated at 02:46 PM ---------- Previous update was at 02:43 PM ----------

Franklin,
the value "0.00" occurs once in every line. there are above 3000 lines in the input pdb file.
# 7  
Old 07-04-2011
Code:
 
$ count=0;while read value;do count=`expr $count + 1`; nawk -v val=$value -v lineno=$count '{ if(NR==lineno){ for(i=1;i<=9;i++){ printf("%s\t",$i);}printf("%s\t%s\n",val,$NF);}}' file1.pdb; done < file2.dat
ATOM    1       C       PHE     1       48.343  23.545  32.02   1.00    20.568  C
ATOM    2       H       HIE     1       48.343  23.545  32.02   1.00    98.346  H
ATOM    3       C       PHE     1       48.343  23.545  32.02   1.00    17.837  C
ATOM    4       N       ALA     1       48.343  23.545  32.02   1.00    14.469  N
ATOM    5       0       VAL     1       48.343  23.545  32.02   1.00    57.537  O

 
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. UNIX for Beginners Questions & Answers

Replace a numeric values in a certain column

Hi All, I am trying to replace a certain value from one place in a file . In the below file at position 35 I will have 8 I need to modify all 8 in that position to 7 I tried awk '{gsub("8","7",$35)}1' infile > outfile ----> not working sed -i 's/8/7'g' infile --- it is replacing all... (3 Replies)
Discussion started by: arunkumar_mca
3 Replies

2. Shell Programming and Scripting

Trying to get an awk script to replace values in column

I'm trying to make an awk script to compare values I've set as var1, var2, and var3 earlier in the script to the values in the userinputted column of four text files called Node1.txt, Node2.txt, Node3.txt, and Node4.txt and then replace the values in that userinputted column with either ttt or gcc,... (8 Replies)
Discussion started by: Eric1
8 Replies

3. UNIX for Dummies Questions & Answers

Replace all decimal values in a column

Hi My input file looks String000002 GeneWise CW 48945 49354 . - 0 Pt=PEQU_00004; String000002 LEN NA 52125 52604 0.945751 - . PID=PEQU_00005;lvid_id=PEQ_28708; String000002 LEN CW 52125 52604 . - 0 ... (3 Replies)
Discussion started by: siya@
3 Replies

4. Shell Programming and Scripting

Replace column values from other file

I have one file as it has the following format File1 S No Site IP Address 1 Australia 192.168.0.1/26 2 Australia 192.168.0.2/26 3 Australia 192.168.0.3/26 I need awk/sed command to replace the column2 value ( under Site) with some other... (8 Replies)
Discussion started by: samaritan
8 Replies

5. Shell Programming and Scripting

Selective Replace awk column values

Hi, I have the following data: 2860377|"DATA1"|"DATA2"|"65343"|"DATA2"|"DATA4"|"11"|"DATA5"|"DATA6"|"65343"|"DATA7"|"0"|"8"|"1"|"NEGATIVE" 32340377|"DATA1"|"DATA2"|"65343"|"DATA2"|"DATA4"|"11"|"DATA5"|"DATA6"|"65343"|"DATA7"|"0"|"8"|"1"|"NEG-DID"... (3 Replies)
Discussion started by: sdohn
3 Replies

6. Shell Programming and Scripting

sed replace values of column with ordered numbering

Hello, I am trying to write a shell script that will create a gnuplot file. My main problem is that I have a data file with two columns: 1.05929120E+09 5.0000701214792 1.05930096E+09 5.00006386985764 1.05930584E+09 5.00019465404908 1.05931072E+09 5.00031960589719 ... (2 Replies)
Discussion started by: pau
2 Replies

7. UNIX for Dummies Questions & Answers

Replace values in a specified column of a file

Hello, I have a file with four columns and I would like to replace values in the second column only. An arbitrary example is: 100 A 105 B 200 B 205 C 300 C 305 D 400 D 405 E 500 E 505 F I need to replace the second column as shown below: ... (4 Replies)
Discussion started by: Gussifinknottle
4 Replies

8. Shell Programming and Scripting

Find and replace duplicate column values in a row

I have file which as 12 columns and values like this 1,2,3,4,5 a,b,c,d,e b,c,a,e,f a,b,e,a,h if you see the first column has duplicate values, I need to identify (print it to console) the duplicate value (which is 'a') and also remove duplicate values like below. I could be in two... (5 Replies)
Discussion started by: nuthalapati
5 Replies

9. Shell Programming and Scripting

replace the column values.

I have the below file ...where some of the column values should replaced with desired values ....below file u can find that 3 column where ever 'AAA' comes should replaced with ' CC ' NOTE : we have to pass the column number ,AAA,CC (modified value) as the parameters to the code. ... (6 Replies)
Discussion started by: charandevu
6 Replies

10. UNIX for Advanced & Expert Users

replace a column values with the first value in column

Hi All, I have a file which has data in following format: "Body_Model","2/1/2007","2/1/2007" "CSCH74","0","61" "CSCS74","0","647" "CSCX74","0","3" "CSYH74","0","299" "CSYS74","0","2514" "CSYX74","0","3" "Body_Model","3/1/2007","3/1/2007" "CSCH74","0","88" "CSCS74","0","489"... (3 Replies)
Discussion started by: sumeet
3 Replies
Login or Register to Ask a Question