Perl: Keep only one of two consecutive characters - regex

Question

I'm having trouble applying a regex to keep only one of two specific consecutive characters in a column. I have the following file in which C-O appears for number 1 and number 2, as indicated. I would like to write a new file in which only C-O in number 1 is present. This functionality needs to be repeated throughout the file, for example between number 2 and 3 (keep number 2), and number 3 and 4 (keep number 3) etc .
Input:
1 H 27.5310
1 H 27.0882
1 C 36.8857
1 O -118.2564
2 C 36.6954
2 O -118.5597
2 N 133.6704
2 H 28.3581
Output:
1 H 27.5310
1 H 27.0882
1 C 36.8857
1 O -118.2564
2 N 133.6704
2 H 28.3581
This is what I have so far, hope my logic is semi-clear. I'm still learning and any commentary is greatly appreciated!
#!/usr/bin/perl
use strict;
use warnings;
my $file = 'data.txt';
open my $fh, '<', $file or die "Can't read $file: $!";
while (my $line = <fh>) {
chomp $line;
my #column = split(/\t/,$line);
if ($column[1] =~ s/COCO/\s+/g) {
print "#columns\n";
}
}

Answer 1

You could maybe do it all at once. Read the whole file into a string.
Then put it through this regex.
# s/(?m)(^\h+(\d+)\h+C.*\s+^\h+\2\h+O.*\n)\s*^\h+(?!\2)(\d+)\h+C.*\s+^\h+\3\h+O.*\n(?!\s*\z)/$1/g
(?xm-)
# C-O in the bottom of a segment
( # (1 start), Keep this
^ \h+ # new line
( \d+ ) # (2), col 1 number
\h+ C .* \s+ # C
^ \h+ # next line
\2 \h+ O .* \n # \2 .. O
) # (1 end)
# Throw this away
# C-O in the top of next segment
\s*
^ \h+ # new line
(?! \2 ) # Not \2
( \d+ ) # (3), col 1 num
\h+ C .* \s+ # C
^ \h+ # next line
\3 \h+ O .* \n # \3 .. O
(?! \s* \z ) # Not the last in file
Perl code:
use strict;
use warnings;
$/ = "";
my $input = <DATA>;
print "Input:\n$input\n";
$input =~
s/(?xm-)
# C-O in the bottom of a segment
( # (1 start), Keep this
^ \h+ # new line
( \d+ ) # (2), col 1 number
\h+ C .* \s+ # C
^ \h+ # next line
\2 \h+ O .* \n # \2 .. O
) # (1 end)
# Throw this away
# C-O in the top of next segment
\s*
^ \h+ # new line
(?! \2 ) # Not \2
( \d+ ) # (3), col 1 num
\h+ C .* \s+ # C
^ \h+ # next line
\3 \h+ O .* \n # \3 .. O
(?! \s* \z ) # Not the last in file
/$1/g;
print "Output:\n$input\n";
__DATA__
1 H 27.5310
1 H 27.0882
1 C 36.8857
1 O -118.2564
2 C 36.6954
2 O -118.5597
2 N 133.6704
2 H 28.3581
Code output:
Input:
1 H 27.5310
1 H 27.0882
1 C 36.8857
1 O -118.2564
2 C 36.6954
2 O -118.5597
2 N 133.6704
2 H 28.3581
Output:
1 H 27.5310
1 H 27.0882
1 C 36.8857
1 O -118.2564
2 N 133.6704
2 H 28.3581