Printing Hash of Arrays

[iangibson]

Hi Monks,

I have the following code, whose purpose is to grab the data from the first two columns (chromosome and coordinate) of a series of files, then output to a new file these pairs ordered by chromosome and coordinate, having removed duplicates of any pairs occurring in more than one input file.

The code I've written so far outputs only one line per chromosome, with all the coordinates in the correct order.

What I'd like to have is each coordinate for a given chromosome to appear on its own next to the chromosome, e.g. where at present I have:

11   608502 1016988 1017495 1018088 3661585

I'd like to instead have:

11    608502 
11    1016988 
11    1017495 
11    1018088 
11    3661585

The other change I'd like to make is to output the chromosomes in numerical order, rather than in hash order as at present. Any help you can offer me would be much appreciated.

#!/usr/bin/perl
use warnings;
use strict;
use v5.10;

#  Create program to read in a series of VCF files, outputting a two-c
+olumn
#  file consisting of chromosome and coordinate for each site seen in 
+one or
#  more files ('master-site-list').

die "Give the names of each VCF" if @ARGV < 1;

my $number_of_files = @ARGV;
my $infile;
my $current_file_number = 0;

my %hash_of_chroms;

open my $outfile, '>', "master-site-list" or die "Cannot open output f
+ile: $!";

until ( $current_file_number >= $number_of_files ) {

    open $infile, '<', $ARGV[$current_file_number]
      or die "Cannot open VCF file: $!";

    while (<$infile>) {
        chomp;
        next if /^#/;

        my ( $chr, $coord ) = split(/\s+/);

        push @{ $hash_of_chroms{$chr} }, $coord
          unless defined $hash_of_chroms{$chr}[$coord];   # don't add 
+duplicates
    }

    $current_file_number++;

    close $infile;

}

my %sorted_hash_of_chroms;
foreach my $chrom ( keys %hash_of_chroms ) {
    push @{ $sorted_hash_of_chroms{$chrom} },
      sort { $hash_of_chroms{$a}->[0] <=> $hash_of_chroms{$b}->[0] }
      keys %hash_of_chroms;
}

foreach my $chrom ( keys %hash_of_chroms ) {
    say $outfile "$chrom\t@{ $hash_of_chroms{$chrom} }";
}

close $outfile;

Examples of input file:

##fileformat=VCFv4.1
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RR,Number=1,Type=Integer,Description="Reference Read Dept
+h">
##FORMAT=<ID=VR,Number=.,Type=Integer,Description="Variant Read Depth(
+s)">
##FORMAT=<ID=PL,Number=.,Type=Integer,Description="Normalized, Phred-s
+caled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=SF,Number=.,Type=String,Description="Source file(s)">
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT 
+   NA19238
1    874816    .    C    CT    10    FINAL_AMBG    SF=bcm_illum,bi_ill
+um;validation_ratio=52/1019;sets=bcm_illum,bi_illum;samples=NA19238  
+  GT    1/0
1    1647893    .    C    CTTTCTT    30    FINAL_NOT_CONFIRMED    SF=b
+cm_illum,bcm_solid;validation_ratio=0/3380;sets=bcm_illum,bcm_solid;s
+amples=NA19238    GT    0/0
1    7889972    rs57875989    GAGAATCCATCCCATCCTACTGCCAGCGCTCTGTCCACAG
+GATCGCCTCCCATGA    G    33190    DESIGN_FAIL    SF=bi_illum    GT    
+./.
1    14106394    .    A    ACTC    100    FINAL_CONFIRMED    SF=bcm_il
+lum,bcm_solid,bc_illum;validation_ratio=864/1754;sets=bcm_illum,bcm_s
+olid,bc_illum;samples=NA19238    GT    1/0

[RichardK]

BTW this bit of code doesn't do what you think it does

        push @{ $hash_of_chroms{$chr} }, $coord
          unless defined $hash_of_chroms{$chr}[$coord];   # don't add 
+duplicates

push adds the item to the end of the list and you check some list element off in the far distance.

i.e. if the array is empty and $coord = 50, then your code does this:-

     $array[0] = $coord unless $array[50];

[Anonymous Monk]

So, you would like to make these changes? Go ahead :)

[Anonymous Monk]

Can you identify where you need to make the changes?