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Home: Perl Programming Help: Intermediate:
Accessing hash of array of arrays

sessmurda
Novice

Jan 5, 2011, 12:20 PM

Post #1 of 2 (516 views)

Accessing hash of array of arrays	Can't Post

Hey all,

I posted this question in a more complicated form before and got no responses. After taking care of a few other things earlier this week I'm back at trying to finish this script. What I want to do is take the data below, and for each hash key, if there are multiple lines where column 4 is equal, and if in those same lines column 5 is equal (both instances also want to set a wobble of + or - 5). If for a hash, there are say 3 instances where the 2 columns give the same values (within the wobble range), then I want to exclude those. Basically I need to know the syntax to access specific elements of a hash of arrays of arrays. The file format is below.

TC356967 Scaffold4333 89.7818599311137 6443 7354 1
TC356967 Scaffold463974 89.3333333333333 7554 8067 -1
TC356967 Scaffold93112 89.3203883495146 7760 8068 1
TC356967 Scaffold174194 89.2733564013841 7781 8068 1
TC356967 Scaffold407210 89.0243902439024 7973 8054 1
TC356967 Scaffold13981 88.9487870619946 7553 8084 1
TC356967 Scaffold363276 88.8888888888889 7760 8083 1
TC356967 Scaffold214368 88.5844748858447 7554 8083 -1
TC356967 Scaffold299965 88.5245901639344 7781 8084 -1
TC356967 Scaffold221597 88.4615384615385 7554 8083 -1
TC356967 Scaffold192663 88.4507042253521 7729 8083 1
TC356967 Scaffold48509 88.4488448844885 7781 8083 1
TC356967 Scaffold88696 88.3668903803132 7554 8083 1
TC356967 Scaffold99960 88.2618510158014 7554 8083 1
TC356967 Scaffold1551 88.1944444444444 7551 8063 -1
TC356967 Scaffold14356 88.1481481481482 7554 8083 -1
TC356967 Scaffold148662 88.0733944954129 7760 8085 1

Code below.

Code

use warnings; 
use Data::Dumper; 
open (IN, "$ARGV[0]") || die "nope\n"; 
my %data; 
while(<IN>) 
{ 
   chomp; 
   my $line = $_; 
   my ($key, $scaf, $perc, $start, $stop, $strand) = (split/\t/, $line); 
   push @{ $data{$key} }, $line; 
 
#foreach $key (keys %data) 
#{ 
#    my ($scaf1, $perc1, $start1, $stop1, $strand1) = @{$data{$name}}; 
#unless ( 
 
#} 
} 
print Dumper(\%data);

Data Dumper prints output like:
'TC383408' => [
'TC383408 Scaffold293195 100 1 132 1',
'TC383408 Scaffold45175 100 130 816 1'
],

Meaning that I am creating the hash of array of arrays fine, but I am unsure how to access the specific elements. Any leads on how to compare specific elements of a hash of arrays of arrays?

Thanks

FishMonger
Veteran

Jan 5, 2011, 1:06 PM

Post #2 of 2 (513 views)

Re: [sessmurda] Accessing hash of array of arrays [In reply to]	Can't Post

That's a HoA (hash of arrays), not a HoAoA (hash of arrays of arrays).

Code

#!/usr/bin/perl 
 
use strict; 
use warnings; 
use Data::Dumper; 
 
my %data; 
 
while ( my $line = <DATA> ) { 
    chomp $line; 
    my ($key, $scaf, $perc, $start, $stop, $strand) = (split/\t/, $line); 
     
    push @{ $data{$key} }, [ $scaf, $perc, $start, $stop, $strand ]; 
} 
 
print Dumper(\%data), "\n"; 
 
foreach my $key ( keys %data ) { 
 
    print $data{$key}[0][1], "\n"; 
} 
 
 
__DATA__ 
TC356967		caffold4333	89.7818599311137	6443	7354	1 
TC356967		caffold463974	89.3333333333333	7554	8067	-1 
TC356967		caffold93112	89.3203883495146	7760	8068	1 
TC356967		caffold174194	89.2733564013841	7781	8068	1 
TC356967		caffold407210	89.0243902439024	7973	8054	1 
TC356967		caffold13981	88.9487870619946	7553	8084	1 
TC356967		caffold363276	88.8888888888889	7760	8083	1 
TC356967		caffold214368	88.5844748858447	7554	8083	-1 
TC356967		caffold299965	88.5245901639344	7781	8084	-1 
TC356967		caffold221597	88.4615384615385	7554	8083	-1 
TC356967		caffold192663	88.4507042253521	7729	8083	1 
TC356967		caffold48509	88.4488448844885	7781	8083	1 
TC356967		caffold88696	88.3668903803132	7554	8083	1 
TC356967		caffold99960	88.2618510158014	7554	8083	1 
TC356967		caffold1551	88.1944444444444	7551	8063	-1 
TC356967		caffold14356	88.1481481481482	7554	8083	-1 
TC356967		caffold148662	88.0733944954129	7760	8085	1

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