How to do alpha numeric sort perl?

Question

I have a file which looks like this:

80,1p21  
81,19q13  
82,6p12.3  
83,Xp11.22  
84,3pter-q21  
86,3q26.33  
87,14q24.1-q24.2|14q24|14q22-q24  
88,1q42-q43  
8         


        

Answer 1

I actually found the answer to this. The code looks a bit complicated though.

#!/usr/bin/env perl

use strict;  
use warnings;

sub main {   
my $file;  
if (@ARGV != 1) {   
    die "Usage: perl hashofhash_sort.pl \n";
}   
else {  
    $file = $ARGV[0];   
}  

open(IN, $file) or die "Error!! Cannot open the $file file: $!\n";
my @file = ;
chomp @file;
my ($entrez_gene, $loci, $chr, $band, $pq, $band_num);
my (%chromosome, %loci_entrez);

foreach my $line (@file) {
    if ($line =~ /(\d+),(.+)/) {
        # Entrez genes
        $entrez_gene = $1;

        # Locus like 12p23.4
        $loci = $2;

        if ($loci =~ /^(\d+)(.+)?/) {
            # chromosome number alone (only numericals)
            $chr = $1;
            if ($2) {
                # locus minus chromosome number. If 12p23.4, then $band is p23.4
                $band = "$2";
                if ($band =~ /^([pq])(.+)/) {
                    # either p or q
                    $pq = $1;
                    # stores the numericals. for p23.4, stores 23.4
                    $band_num = $2;
                }

                if (exists $chromosome{$chr}) {
                    if (exists $chromosome{$chr}{$pq}) {
                        push (@{$chromosome{$chr}{$pq}}, $band_num);
                    }
                    else {
                        $chromosome{$chr}{$pq} = [$band_num];
                    }
                }

                else {
                    $chromosome{$chr}{$pq} = [$band_num];
                }
            }
        }
    }
} # End of foreach loop

foreach my $key (sort {$a <=> $b} keys %chromosome) {
    my %seen = ();
    foreach my $key2 (sort {$a cmp $b } keys %{$chromosome{$key}}) {
        my @unique = grep { ! $seen{$_}++ } @{$chromosome{$key}{$key2}};
        my @sorted = sort @unique;
        foreach my $element (@sorted) {
            my $sorted_locus = "$key$key2$element";
            if (exists $loci_entrez{$sorted_locus}) {
                foreach my $element2 (@{$loci_entrez{$sorted_locus}}) {
                        print "$element2,$sorted_locus\n";

                }
            }
        }
    }

}


} # End of main

main();