Hi Perl Monks

I have got 2 files where in file1 (sample.txt) it is the list of samples IDs (which is around 1000). These sample IDs are the column name in the file2 (sampleValue.txt). The file2 is a data matrix of 30000*1500. I am interested in values of all the rows in 1000 columns out of 1500 which are like 1,2,5,6,70,71,75,100,112,114 and so on. There is no pattern on the columns. So, here is what I am doing and would like to know how can I improve it. Here is my code:

 
use strict;
use warnings;

## Variables
my %sampleID;
my %sampleValue;


## Opening first file
open my $IN, "sample.txt" or die $!;
my $header = <$IN>;

while(<$IN>){
    chomp $_;
    my @line = split('\t', $_);
    $sampleID{$line[0]} = 1; ## Sample ID and Pam50 prediction
}
close($IN);
print "Total number of sample ID: ", scalar(keys %sampleID),"\n"; ## 1
+000 columns

## Sample Value Data
open $IN, "sampleValue.txt" or die $!;

## Columns are sample names from file1
$header = <$IN>;
my @samples = split("\t", $header); ## 
print "Total samples: ",scalar(@samples),"\n"; ## 1500

## loop for all the samples ids or the columns I am interested in
for(my $i = 1; $i <= $#samples; $i++){ ## bcos the first instance is c
+alled header of the column 1
    my $sample = $samples[$i];
    $sampleValue{$sample} = $i if (exists $sampleID{$sample});
}

my $col = "";  
foreach my $key (keys %sampleValue){
    $col = $sampleValue{$key}.",".$col;
}
chop($col);
print $col,"\n"; ## string of all the columns I am interested in

## The reason I do the above loop because I don't want to look for the
+ interested ## cols thru the hash for every line of the file

## Reading the sample Value file
while(<$IN>){
    chomp $_;
    print $_,"\n";
    my @line = split("\t", $_);
    @line = @line[ split /,/, $col]; ## previously it was @line = @lin
+e[$col] -- and i was getting error because $col is a string
    print @line,"\n";
}

[download]

So, my question is whether there is an easy way to convert the string $col to numeric cols with commas in it or a better way to get the desired columns ?

UPDATE: I have updated my code. May me it will be of some use to people later.

In reply to Extracting Columns from line by snape

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