perl to remove lines from file

Question

I have file that looks like:

ATOM 2517 O   VAL 160 8.337  12.679  -2.487
ATOM 2518 OXT VAL 160 7.646  12.461  -0.386
TER 
ATOM 2519 N   VAL 161 -14.431  5.789 -2         


        

Answer 1

A simple line-by-line script.

Usage: perl script.pl -i.bak fileglob

E.g. perl script.pl -i.bak File*MINvac.pdb

This will alter the original file, and save a backup of each file with the extension .bak. Note that if TER lines appear too close to the end of the file, it will cause warnings. On the other hand, so will the other solutions presented.

If you do not wish to save backups (use caution, since changes are irreversible!), use -i instead.

Code:

#!/usr/bin/perl
use v5.10;
use strict;
use warnings;

my $prev;
while (<>) {
    if (/^TER/) {
        print scalar <>;  # print next line
        <> for 1 .. 3;    # skip 3 lines
        $prev = undef;    # remove previous line
    } else {
        print $prev if defined $prev;
        $prev = $_;
    }
    if (eof) {  # New file next iteration?
        print $prev;
        $prev = undef;
    }
}