I can't figure out how to apply this subroutine (pretty_print) to my data:

#!/usr/bin/perl
use warnings;
#use strict;

($sfile_1, $sfile_2) = @ARGV;

($id1, $seq1) = read_fasta($sfile_1);
($id2, $seq2) = read_fasta($sfile_2);

pretty_print(\$id1, \$seq1);
pretty_print(\$id2, \$seq2);

sub read_fasta {
        ## reads a single sequence from a fasta file
    my $seqFile = shift @_;
    my $seq = "";
    my $id = "";
    open(my $in, "<", $seqFile) or die "unable to open $seqFile $!\n";
    while(<$in>){
        chomp;
        if($_ =~ /^>(\S+)/ ){
        last if(length($id));
        $id = $1;
        next;
    }
        if(length($id)){
        $seq .= $_;
        }
    }
    return ($id, $seq);
}

sub pretty_print {
    my($seq, $colno) = shift @_;
    # We want to start from 0, and increment the starting position.
    # for this we use a classical loop.
    for (my $b=0; $b < length($seq); $b += $colno){
        print( substr($seq, $b, $colno), "\n");
    }
}

exit;

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The two data files if needed: https://justpaste.it/1ch48 and https://justpaste.it/1ch4b

In reply to How to use this subroutine by bisimen

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