Re: Population of HoAoA based on file contents

[iangibson]

Okay, I think I've made some progress, but I'm still not quite there yet. Here's what I now have:

#!/usr/bin/perl
use warnings;
use strict;
use v5.14;

use Getopt::Long;
use Bio::PopGen::IO;
use Bio::PopGen::Statistics;

die "need two arguments (i.e. chr cont) at invocation" unless @ARGV ==
+ 2;

chomp( my $chr_num = shift );
chomp( my $cont    = shift );

open my $out_file, ">", "chr${chr_num}_exome_snps_processed_${cont}_ST
+ATS"
  or die "Can't open output file: $!\n";

open my $in_file, "<", "chr${chr_num}_exome_snps_processed_$cont"
  or die "Can't open input file: $!\n";

my %data;
my @snp_bins;
my @individuals;
my @all_snps;

while (<$in_file>) {
    chomp;
    if (/^SAMPLE/) {
        my ( $placeholder, @coords ) = split /,/;
        foreach my $coord (@coords) {
            push @snp_bins, int( $coord / 100_000 );
        }
    }
    else {
        my ( $id, @snps ) = split /,/;
        push @individuals, $id;
        push @all_snps[$. - 2], join(',', @snps);
    }
}

foreach my $individual (@individuals) {
    foreach my $index ( 0 .. $#snp_bins ) {
        push( @{ $data{$individual}[ $snp_bins[$index] ] }, $all_snps[
+$index] );
    }
}

close $in_file;

But there's still (at least) a problem with the line

push @all_snps[$. - 2], join(',', @snps);

I hope I'm otherwise headed in the right direction..?

In regard to what I will do with undefined bins: I will iterate through all the bins, and any that don't have a minimum number of elements simply won't be passed as data to the bioperl popgen stats methods, later on in the program.

[state-o-dis-array]

It seems to me that this would do what you are trying to accomplish.

while (<$in_file>) {
    chomp;
    if (/^SAMPLE/) {
        my ( $placeholder, @coords ) = split /,/;
        foreach my $coord (@coords) {
            push @snp_bins, int( $coord / 100_000 );
        }
    }
    else {
        my ( $id, @snps ) = split /,/;
#need to check here that $#snps == $#snp_bins ?
        foreach my $index ( 0 .. $#snp_bins ) {
          push( @{ $data{$id}[ $snp_bins[$index] ] }, $snps[$index] );
        }
    }
}

Unless you need them elsewhere, I don't see a reason in your code snippent to store @individuals and @all_snps. The "need to check" comment above is based on my attempt to understand your last statement above. If it's possible that @snps might not have an entry for each @snp_bins, then you'll want this check.