perl to remove lines from file - perl

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 -25.371
ATOM 2520 H1 VAL 161 -15.336 5.698 -25.811
ATOM 2521 H2 VAL 161 -13.416 10.529 17.708
ATOM 2522 H3 VAL 161 -14.363 9.436 18.498
ATOM 2523 CA VAL 161 4.400 9.233 16.454
ATOM 2524 HA VAL 161 3.390 9.170 16.047
I have to remove "TER", the line before "TER" and 3 lines after the line just after TER and make file continuous like this:
ATOM 2517 O VAL 160 8.337 12.679 -2.487
ATOM 2519 N VAL 161 -14.431 5.789 -25.371
ATOM 2523 CA VAL 161 4.400 9.233 16.454
ATOM 2524 HA VAL 161 3.390 9.170 16.047

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;
}
}

Answer 2

I realized I was supposed to write it in Perl, but now I've already written it in Python. I'm posting it anyway as it may prove to be useful, don't see any harm in that.
#!/usr/bin/python2.7
import sys
import glob
import os
try:
dir = sys.argv[1]
except IndexError:
print "Usage: "+sys.argv[0]+" dir"
print "Example: "+sys.argv[0]+" /home/user/dir/"
sys.exit(1)
for file in glob.glob(os.path.join(dir, 'File*_*MINvac.pdb')):
fin = open(file, "r")
content = fin.readlines()
fin.close()
for i in range(0, len(content)):
try:
if "TER" in content[i]:
del content[i]
del content[i-1]
del content[i:i+3]
except IndexError:
break
fout = open(file, "w")
fout.writelines(content)
fout.close()
Edit: Added support for multiple files, like the OP wanted.

Answer 3

So, for each set of 6 consecutive lines, you want to discard all but the third line if the second line is a TER?
TIMTOWTDI, but this should work:
my #queue;
while (<>) {
push #queue, $_;
#queue = $queue[2] if #queue == 6 and $queue[1] =~ /^TER$/;
print shift #queue if #queue == 6;
}
print #queue; # assume no TERs in last 4 lines

Answer 4

use strict;
use warnings;
use Tie::File;
my #array;
tie #array, 'Tie::File', 'myFile.txt' or die "Unable to tie file";
my %unwanted = map { $_ => 1 } # Hashify ...
map { $_-1, $_, $_+2 .. $_+4 } # ... the five lines ...
grep { $array[$_] =~ /^TER/ } # ... around 'TER' ...
0 .. $#array ; # ... in the file
# Remove the unwanted lines
#array = map { $array[$_] } grep { ! $unwanted{$_} } 0 .. $#array;
untie #array; # The end