Question

I am working in linux bash environment, and I have many files to edit, 900 or so.
In one file,filename.txt, I have list of file names, one file name per line.
for example

ab2.pdb.101
ab2.pdb.109
ab2.pdb.126
ab2.pdb.127
ab2.pdb.13
ab2.pdb.187
ab2.pdb.188

and the first few lines of context of these files are like,(total of 245 lines)

REMARK   1                     PDB file generated by ptraj (set    33)
ATOM      1  N   ALA     1      11.304   3.018  20.878  0.1414  1.8240
ATOM      2  H1  ALA     1      11.574   3.686  21.593  0.1997  0.6000
ATOM      3  H2  ALA     1      11.901   3.162  20.074  0.1997  0.6000
ATOM      4  H3  ALA     1      10.342   3.207  20.625  0.1997  0.6000
ATOM      5  CA  ALA     1      11.449   1.637  21.381  0.0962  1.9080
ATOM      6  HA  ALA     1      12.509   1.464  21.561  0.0889  1.1000

I would like to replace the last two columns of numers from second line to the end of file with 0.0000 0.0000

0.1414  1.8240
0.1997  0.6000
0.1997  0.6000
0.1997  0.6000
0.0962  1.9080
0.0889  1.1000

to

0.0000  0.0000
0.0000  0.0000
0.0000  0.0000
0.0000  0.0000
0.0000  0.0000
0.0000  0.0000

So I would like to read in a file which file names are in one text file named “filenames.txt” and replace last two column numbers to 0.0000.

Thank you all for any help.

Answer 1

This code uses head to get the first line, tail to get the rest, cut to get only the starting columns, paste to add additional columns, (these two assume tab is used to separate columns), yes to generate the columns.

#! /bin/bash
while read file ; do {
        head -n1 "$file"
        tail -n+2 "$file" | \
            cut -f1-8 | \
            paste - <( yes 0.0000$'\t'0.0000 | \
            head -n $(( $( wc -l < "$file")-1 ))
        )
    }  > "$file".new
done < filenames.txt

Update:
If the structure of the files is more complicated, I would use something more comfortable than bash. For example, this is how to do it in Perl:

#!/usr/bin/perl
use warnings;
use strict;

open my $NAMES, '<', 'filenames.txt' or die $!;
for my $file (<$NAMES>) {
    chomp $file;
    open my $FILE, '<', $file or die $!;
    open my $NEW,  '>', "$file.new" or die $!;
    print {$NEW} scalar <$FILE>;               # print 1st line
    while (<$FILE>) {
        my @fields = split /(\s+)/;            # keep separators
        @fields[-4, -2] = ('0.0000') x 2;      # replace the last two non-whitespace columns
        print {$NEW} @fields;
    }
}