add a number to a column in a text file -- linux awk-CodePudding

Im attempting to add the number 128 to each line containing a number of column 6 of my file. When I use

awk '{ $6 =128; print }1' below_zn.pdb

I am able to do this, but the formatting of my file changes. I need to keep the formatting. I have tried

awk -F'()' '{ $6 =128; print }' below_zn.pdb

but instead of adding the number 128 to my column 6 numbers, I am seeing a new column at the farthest right made of the number 128 repeatedly. Is there a way I can use awk/sed/grep to add 128 to my numbers in column 6 while keeping the formatting as follows:

ATOM      1  ZN  ZN2 H   1     -13.264  34.400  10.700  1.00  0.00      HETA  
ATOM      2  ZN  ZN2 H   2     -13.264  25.273  10.700  1.00  0.00      HETA  
ATOM      3  ZN  ZN2 H   3     -13.264  43.527  10.700  1.00  0.00      HETA  
ATOM      4  ZN  ZN2 H   4     -13.264  52.654  10.700  1.00  0.00      HETA  
ATOM      5  ZN  ZN2 H   5     -13.175  29.836  14.467  1.00  0.00      HETA

Thank you!

CodePudding user response：

Assumptions:

input is using fixed-width spacing
white space only shows up as a column delimiter (ie, no column values contain white space)
the values in column 6 are left-justified

Adding a new row to demonstrate a wider value for column 6:

$ cat below_zn.pdb
ATOM      1  ZN  ZN2 H   1     -13.264  34.400  10.700  1.00  0.00      HETA
ATOM      2  ZN  ZN2 H   2     -13.264  25.273  10.700  1.00  0.00      HETA
ATOM      3  ZN  ZN2 H   3     -13.264  43.527  10.700  1.00  0.00      HETA
ATOM      4  ZN  ZN2 H   4     -13.264  52.654  10.700  1.00  0.00      HETA
ATOM      5  ZN  ZN2 H   5     -13.175  29.836  14.467  1.00  0.00      HETA
BUBBLE  206  ZN  ZN2 H   7000  -13.175  29.836  14.467  1.00  0.00      HETA-HETA

One awk idea:

awk '
BEGIN { regex1="^([^[:space:]] [[:space:]] ){5}"                  # match 1st 5 columns plus trailing white space
        regex2="[^[:space:]] "                                    # match non-white space characters (aka 6th column)
      }
      { oldline=$0

        match(oldline,regex1)                                     # find 1st 5 columns
        newline=substr(oldline,1,RSTART RLENGTH-1)                # save 1st 5 columns for new line
        oldline=substr(oldline,RSTART RLENGTH)                    # strip off 1st 5 columns

        match(oldline,regex2)                                     # match 1st column of shortened line (aka 6th column of original line)
        newval=substr(oldline,1,RLENGTH)   128                    # extract column and add 128
        newlen=length(newval)                                     # get length of new value
        newline=newline newval substr(oldline,RSTART newlen)      # append new value and rest of line to newline

        print newline                                             # print newline to stdout
      }
' below_zn.pdb

This generates:

ATOM      1  ZN  ZN2 H   129   -13.264  34.400  10.700  1.00  0.00      HETA
ATOM      2  ZN  ZN2 H   130   -13.264  25.273  10.700  1.00  0.00      HETA
ATOM      3  ZN  ZN2 H   131   -13.264  43.527  10.700  1.00  0.00      HETA
ATOM      4  ZN  ZN2 H   132   -13.264  52.654  10.700  1.00  0.00      HETA
ATOM      5  ZN  ZN2 H   133   -13.175  29.836  14.467  1.00  0.00      HETA
BUBBLE  206  ZN  ZN2 H   7128  -13.175  29.836  14.467  1.00  0.00      HETA-HETA

CodePudding user response：

You may try rq (https://github.com/fuyuncat/rquery/releases). Use a dynamic variable to pass the new column, and regreplace to replace the column and keep the original format.

[ rquery]$ ./rq -v "v:0:@6 128" -q "p d/ /r | s regreplace(@raw,'(^\S [ ] \S [ ] \S [ ] \S [ ] \S [ ] )(\S )(.*)','\$1' @v '\$3')" samples/below_zn.pdb -m error
ATOM      1  ZN  ZN2 H   129     -13.264  34.400  10.700  1.00  0.00      HETA
ATOM      2  ZN  ZN2 H   130     -13.264  25.273  10.700  1.00  0.00      HETA
ATOM      3  ZN  ZN2 H   131     -13.264  43.527  10.700  1.00  0.00      HETA
ATOM      4  ZN  ZN2 H   132     -13.264  52.654  10.700  1.00  0.00      HETA
ATOM      5  ZN  ZN2 H   133     -13.175  29.836  14.467  1.00  0.00      HETA