replace a column with values from another file


 
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# 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:
# 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

 
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