Add new hash keys and then print in a new file - perl

Question

Previously, I post a question to search for an answer to using regex to match specifics sequence identification (ID).
Now I´m looking for some recommendations to print the data that I looking for.
If you want to see the complete file, here's a GitHub link.
This script takes two files to work. The first file is something like this (this is only a part of the file):
AGY29650_2_NA netOGlyc-4.0.0.13 CARBOHYD 2 2 0.0804934 . .
AGY29650_2_NA netOGlyc-4.0.0.13 CARBOHYD 4 4 0.0925522 . .
AGY29650_2_NA netOGlyc-4.0.0.13 CARBOHYD 13 13 0.0250116 . .
AGY29650_2_NA netOGlyc-4.0.0.13 CARBOHYD 23 23 0.565981 . .
...
This file tells me when there is a value >= 0.5, this information is in the sixth column. When this happens my script takes the first column (this is an ID, to match in with the second file) and the fourth column (this is a position of a letter in the second file).
Here my second file (this is only a part):
>AGY29650.2|NA spike protein
MTYSVFPLMCLLTFIGANAKIVTLPGNDA...EEYDLEPHKIHVH*
Like I said previously, the script takes the ID in the first file to match with the ID in the second file when these are the same and then searches for the position (fourth column) in the contents of the data.
Here an example, in file one the fourth row is a positive value (>=0.5) and the position in the fourth column is 23.
Then the script searches for position 23 in the data contents of the second file, here position 23 is a letter T:
MTYSVFPLMCLLTFIGANAKIV T LP
When the script match with the letter, the looking for 2 letters right and 2 letters left to the position of interest:
IVTLP
In the previous post, thank the help of some people in Stack I could solve the problem because of a difference between ID in each file (difference like this: AGY29650_2_NA (file one) and AGY29650.2 (file two)).
Now I looking for help to obtain the output that I need to complete the script.
The script is incomplete because I couldn't found the way to print the output of interest, in this case, the 5 letters in the second file (one letter of the position that appears in file one) 2 letters right, and 2 left.
I have thousands of files like the one and two, now I need some help to complete the script with any idea that you recommend.
Here is the script:
use strict;
use warnings;
use Bio::SeqIO;
​
my $file = $ARGV[0];
my $in = $ARGV[1];
my %fastadata = ();
my #array_residues = ();
my $seqio_obj = Bio::SeqIO->new(-file => $in,
-format => "fasta" );
while (my $seq_obj = $seqio_obj->next_seq ) {
my $dd = $seq_obj->id;
my $ss = $seq_obj->seq;
###my $ee = $seq_obj->desc;
$fastadata{$dd} = "$ss";
}
​
my $thres = 0.5; ### Selection of values in column N°5 with the following condition: >=0.5
​
# Open file
open (F, $file) or die; ### open the file or end the analyze
while(my $one = <F>) {### readline => F
$one =~ s/\n//g;
$one =~ s/\r//g;
my #cols = split(/\s+/, $one); ### split columns
next unless (scalar (#cols) == 7); ### the line must have 7 columns to add to the array
my $val = $cols[5];
​
if ($val >= 0.5) {
my $position = $cols[3];
my $id_list = $cols[0];
$id_list =~ s/^\s*([^_]+)_([0-9]+)_([a-zA-Z0-9]+)/$1.$2|$3/;
if (exists($fastadata{$id_list})) {
my $new_seq = $fastadata{$id_list};
my $subresidues = substr($new_seq, $position -3, 6);
}
}
}
close F;
I´m thinking in add a push function to generate the new data and then print in a new file.
My expected output is to print the position of a positive value (>=0.5), in this case, T (position 23) and the 2 letters right and 2 letters left.
In this case, with the data example in GitHub (link above) the expected output is:
IVTLP
Any recommendation or help is welcome.
Thank!

Answer 1

Main problem seems to be that the line has 8 columns not 7 as assumed in the script. Another small issue is that the extracted substring should have 5 characters not 6 as assumed by the script. Here is a modified version of the loop that works for me:
open (F, $file) or die; ### open the file or end the analyze
while(my $one = <F>) {### readline => F
chomp $one;
my #cols = split(/\s+/, $one); ### split columns
next unless (scalar #cols) == 8; ### the line must have 8 columns to add to the array
my $val = $cols[5];
if ($val >= 0.5) {
my $position = $cols[3];
my $id_list = $cols[0];
$id_list =~ s/^\s*([^_]+)_([0-9]+)_([a-zA-Z0-9]+)/$1.$2|$3/;
if (exists($fastadata{$id_list})) {
my $new_seq = $fastadata{$id_list};
my $subresidues = substr($new_seq, $position -3, 5);
print $subresidues, "\n";
}
}
}