How to print same row data in multiple time from pdb file in perl - perl

Question

I am new in perl, I ma trying to write a program to input pdb file (from Directory, I have 3000 files) and output will save another directory (Another folder).
Code:
open( filehandler, "Document1.txt" ) or die $!; #Input file
my #file1 = <filehandler>;
my $OutputDir = 'C:\test_result_file';
foreach my $line (#file1) {
chomp $line;
open( fh, "$line" ) or die $!;
open( out, ">$OutputDir/$line.pdb" ) or die $!;
while ( $file = <fh> ) {
if ( $file =~ /^ATOM.{9}(?:CG|CD1|CD2B|CE1|CE2|CZ|C|O|CB|CG|CD)/ ) {
$hash{$1}{$2}++;
}
foreach $key ( sort { $hash{$1} <=> $hash{$2} or $1 cmp $2 } keys %hash ) {
print out $key;
}
}
print "Completed", "\n";
}
for example input file:
ATOM 1752 CG TYR A 248 89.088 39.843 51.944 1.00 32.03 C
ATOM 1753 CD1 TYR A 248 89.759 39.356 50.810 1.00 37.15 C
ATOM 1754 CD2 TYR A 248 87.727 40.049 51.864 1.00 32.81 C
ATOM 1755 CE1 TYR A 248 89.078 39.081 49.646 1.00 36.00 C
ATOM 1756 CE2 TYR A 248 87.035 39.774 50.706 1.00 35.66 C
ATOM 1757 CZ TYR A 248 87.708 39.285 49.599 1.00 35.16 C
ATOM 7394 C GLN B 331 37.664 74.934 36.854 1.00 22.75 C
ATOM 7395 O GLN B 331 37.728 73.730 36.607 1.00 31.73 O
ATOM 7396 CB GLN B 331 37.467 76.222 34.712 1.00 27.88 C
ATOM 7397 CG GLN B 331 36.515 76.825 33.693 1.00 32.42 C
ATOM 7398 CD GLN B 331 35.390 75.877 33.328 1.00 35.70 C
Expected output:
A chain:
ATOM 1753 CD1 TYR A 248 89.759 39.356 50.810 1.00 37.15 C
ATOM 1752 CG TYR A 248 89.088 39.843 51.944 1.00 32.03 C
ATOM 1754 CD2 TYR A 248 87.727 40.049 51.864 1.00 32.81 C
ATOM 1755 CE1 TYR A 248 89.078 39.081 49.646 1.00 36.00 C
ATOM 1753 CD1 TYR A 248 89.759 39.356 50.810 1.00 37.15 C
ATOM 1754 CD2 TYR A 248 87.727 40.049 51.864 1.00 32.81 C
ATOM 1755 CE1 TYR A 248 89.078 39.081 49.646 1.00 36.00 C
ATOM 1756 CE2 TYR A 248 87.035 39.774 50.706 1.00 35.66 C
ATOM 1754 CD2 TYR A 248 87.727 40.049 51.864 1.00 32.81 C
ATOM 1755 CE1 TYR A 248 89.078 39.081 49.646 1.00 36.00 C
ATOM 1756 CE2 TYR A 248 87.035 39.774 50.706 1.00 35.66 C
ATOM 1757 CZ TYR A 248 87.708 39.285 49.599 1.00 35.16 C
B chain:
ATOM 7394 C GLN B 331 37.664 74.934 36.854 1.00 22.75 C
ATOM 7395 O GLN B 331 37.728 73.730 36.607 1.00 31.73 O
ATOM 7396 CB GLN B 331 37.467 76.222 34.712 1.00 27.88 C
ATOM 7397 CG GLN B 331 36.515 76.825 33.693 1.00 32.42 C
ATOM 7395 O GLN B 331 37.728 73.730 36.607 1.00 31.73 O
ATOM 7396 CB GLN B 331 37.467 76.222 34.712 1.00 27.88 C
ATOM 7397 CG GLN B 331 36.515 76.825 33.693 1.00 32.42 C
ATOM 7398 CD GLN B 331 35.390 75.877 33.328 1.00 35.70 C
ATOM 7396 CB GLN B 331 37.467 76.222 34.712 1.00 27.88 C
ATOM 7397 CG GLN B 331 36.515 76.825 33.693 1.00 32.42 C
ATOM 7398 CD GLN B 331 35.390 75.877 33.328 1.00 35.70 C
ATOM 7394 C GLN B 331 37.664 74.934 36.854 1.00 22.75 C
Chain ID may be a to h. so, rule is see above expected output: First four row will unique and then line five will be same row of second row and will add new row as eight line row.
I am unable to write a code to solve this problem, any one pl help

Answer 1

I'm afraid I have to say your code is rather confusing but what I get from the data samples and further explanation is:
There should be a window of four lines moving through the input lines.
The window contents (all four lines) should be printed as you advance to each new line.
The window should be reset each time a new sequence is encountered.
Each line is a series of space delimited fields and the fifth field identifies the sequence.
The window contents can be stored in a simple Perl array (see #window in the snippet below). You simply append data to it with push and remove the first line with shift as you move to a next line. When the sequence changes, print the current window and reset it. In the sample code below I made an assumption that sequences do not intermix. If this is note the case, you need to read all the input beforehand and sort it as necessary.
use strict;
use warnings;
my $win_len = 4;
my #window = ();
my $prev_chain = "";
while (<>) {
my ($atom_name, $chain) = (split)[2, 4];
next unless $atom_name =~ /\b(?:CG|CD1|CD2B|CE1|CE2|CZ|C|O|CB|CG|CD)\b/;
if ($chain eq $prev_chain) {
if (#window == $win_len) {
print_window();
shift #window;
}
push #window, $_;
} else {
print_window() if #window;
#window = ($_);
$prev_chain = $chain;
}
}
print_window() if #window;
sub print_window {
print foreach #window;
print "\n";
}
Demo: https://ideone.com/oOB8bF
The script reads data from STDIN and prints result to STDOUT for the sake of simplicity. Your code sample suggests you store a list of files to process in the Document1.txt and the actual input is read from these files. In this case you need an extra loop:
use strict;
use warnings;
my $OutputDir = 'C:/test_result_file';
open my $dir, "Document1.txt" or die "Failed to open Document1.txt:$!";
chomp(my #files = <$dir>);
foreach my $file (#files) {
my $win_len = 4;
my #window = ();
my $prev_chain = "";
open my $input, $file or die "failed to open $file: $!\n";
open my $output, '>', "$OutputDir/$file.pdb" or die "failed to open $OutputDir/$file.pdb: $!\n";
while (<$input>) {
my ($atom_name, $chain) = (split)[2, 4];
next unless $atom_name =~ /\b(?:CG|CD1|CD2B|CE1|CE2|CZ|C|O|CB|CG|CD)\b/;
if ($chain eq $prev_chain) {
if (#window == $win_len) {
print_window($output, #window);
shift #window;
}
push #window, $_;
} else {
print_window($output, #window) if #window;
#window = ($_);
$prev_chain = $chain;
}
}
print_window($output, #window) if #window;
}
sub print_window {
my $fh = shift;
print $fh $_ foreach #_;
print $fh "\n";
}