Anonymous Monk has asked for the wisdom of the Perl Monks concerning the following question:

Hello monks!
I have an array like the following:
ID	ORGANISM	NUMBER
protein1	organism1	0.843534
protein2	organism2	2.45
protein3	organism3	9.5322
protein4	organism4	0.3475474
protein1	organism6	9.4534
protein2	organism7	0.43534
protein2	organism8	1.2434
protein3	organism9	0.000003
protein3	orgnanism10	1.23325
The elements in the array are split with tabs. What I want to do is make a unique array that will hold only protein1, protein2, protein3 and protein4 and, if a protein is found more than once, I will hold the one that has the smallest number.
The desired output is, for the above example:
protein1	organism1	0.843534
protein2	organism7	0.43534
protein3	organism9	0.000003
protein4	organism4	0.3475474
I tried searching the manual, but I have the problem of how to check the numbers and compare them in order to decide which number to keep for each protein...
Thank you for any help!

Replies are listed 'Best First'.
Re: create unique array
by GrandFather (Saint) on Jan 27, 2007 at 09:52 UTC

    "unique == hash". Consider:

    use strict;
use warnings;
use Data::Dump::Streamer;

my @array = <DATA>;

chomp @array;

my %uniq;

for (@array) {
     my @parts = split "\t";
     
     next if @parts < 3;
     next if exists $uniq{$parts[0]} and $uniq{$parts[0]}{val} < $part
+s[2];
     $uniq{$parts[0]} = {val => $parts[2], data => $_};
}

Dump (\%uniq);

__DATA__
protein1    organism1    0.843534
protein2    organism2    2.45
protein3    organism3    9.5322
protein4    organism4    0.3475474
protein1    organism6    9.4534
protein2    organism7    0.43534
protein2    organism8    1.2434
protein3    organism9    0.000003
protein3    orgnanism10    1.23325

    [download]

    Prints:

    $HASH1 = {
           protein1 => {
                         data => "protein1\torganism1\t0.843534",
                         val  => 0.843534
                       },
           protein2 => {
                         data => "protein2\torganism7\t0.43534",
                         val  => 0.43534
                       },
           protein3 => {
                         data => "protein3\torganism9\t0.000003",
                         val  => 0.000003
                       },
           protein4 => {
                         data => "protein4\torganism4\t0.3475474",
                         val  => 0.3475474
                       }
         };

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Re: create unique array
by virtualsue (Vicar) on Jan 27, 2007 at 09:39 UTC
    Your task can be more easily handled by using a hash rather than an array. When you say that the data is in an tab-separated array, do you mean that you have a file which consists of tab-separated lines containing the data? Since you only want to keep one entry for each ID, then a hash containing a reference to an array holding the organism and number values will be a good way to go. Do you have any code we can help you with? Check out the Tutorials section if you need to read up on the data types.

    Update: A skeleton which will read in your data line by line... 

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

my %proteins;

while (my $line = <DATA>) {
  chomp $line;
  my ($pro, $org, $value) = split '\s+, $line;  # \s+ : one or more wh
+itespace chars
}

__DATA__
protein1    organism1    0.843534
protein2    organism2    2.45
protein3    organism3    9.5322
protein4    organism4    0.3475474
protein1    organism6    9.4534
protein2    organism7    0.43534
protein2    organism8    1.2434
protein3    organism9    0.000003
protein3    orgnanism10    1.23325

    [download]
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Re: create unique array
by johngg (Canon) on Jan 27, 2007 at 12:46 UTC
    As virtualsue and GrandFather have advised, a hash is the way to go. You can always recreate an array from your hash afterwards if you need to. The code below uses a form of Schwartzian Transform and works by getting the three elements from each data line then sorting the data lines in descending numerical order on the number field. Thus, for whichever protein/organism combination, the smallest will come last. Finally, the sorted line items are placed in turn into the hash, successively smaller values overwriting any previous larger "duplicates". I then rebuild an array at this point but that may not be what you actually want.

    use strict;
use warnings;

my %smallest =
   map  {
            $_->[0] => {
               org => $_->[1],
               val => $_->[2] }
        }
   sort { $b->[2] <=> $a->[2] }
   map  { chomp; [ split m{\t} ] }
   <DATA>;

my @sorted = ();
foreach my $protein ( sort keys %smallest )
{
    push @sorted, [
       $protein,
       $smallest{$protein}->{org},
       $smallest{$protein}->{val} ];
}

print Data::Dumper->Dump([\@sorted], [qw{*sorted}]);

__END__
protein1    organism1    0.843534
protein2    organism2    2.45
protein3    organism3    9.5322
protein4    organism4    0.3475474
protein1    organism6    9.4534
protein2    organism7    0.43534
protein2    organism8    1.2434
protein3    organism9    0.000003
protein3    orgnanism10    1.23325

    [download]

    Here's the output

    @sorted = (
            [
              'protein1',
              'organism1',
              '0.843534'
            ],
            [
              'protein2',
              'organism7',
              '0.43534'
            ],
            [
              'protein3',
              'organism9',
              '0.000003'
            ],
            [
              'protein4',
              'organism4',
              '0.3475474'
            ]
          );

    [download]

    I hope this is of use.

    Cheers,

    JohnGG

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      Thank you all guys for your help!
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