Greetings,
Howdy.
I've created a hash from an INPUT file and I'm trying to search for each key from the hash in a DATA file.
I'm a little fuzzy on this part, but will see if I can figure it out.
However, I can't get my script to iteratively loop through the DATA file for each key. Instead it loops through DATA once for the first key. Below is some sample data, intended output, and my code. Thank you for any help.
Well, if you want to go back over the DATA for each gene, you need to reopen that file each time to start over.
David
INPUT... ID1 TEST1 ID2 TEST2 ID3 TEST3 ID4 TEST4 ID5 TEST5 ID6 TEST6 ID7 TEST7
DATA... 1 (GN ID ID LKJLSKJLDK) 2 (GN ID ID5 LKJLSKJLDK) 3 (GN ID LKJLSKJLDK ID3) 4 (GN ID2 ID LKJLSKJLDK) 5 (GN ID ID9 LKJLSKJLDK) 6 (GN ID1 ID LKJLSKJLDK) 7 (GN ID ID8 LKJLSKJLDK) 8 (GN ID0 ID LKJLSKJLDK) 9 (GN ID ID4 LKJLSKJLDK)
OUTPUT is: ID1 6 TEST1
OUTPUT should be: ID1 6 TEST1 ID2 4 TEST2 ID3 3 TEST3 ID4 9 TEST4 ID5 2 TEST5
MY CODE...
I suggest adding:
use strict; use warnings;
Write good code, stay sane longer and get better help from us. Win, win, win.
I assume this is a code fragment and that at least one open statement was omitted here, just FYI.
my %genedex;
foreach $line (<INPUT>) {
Don't do that. The foreach reads the whole file into memory and then walks it line by line. If we just want one at a time, let's fetch them that way:
while (defined(my $line = <INPUT>)) {
my ($gene_name,$remainder) = split(/\t/,$line,2); $genedex{$gene_name} = $remainder; }
foreach $gene (sort keys %genedex) {
You should reopen DATA right here each time through the loop, if you want to start over with it:
open DATA, '<path/to/file.txt' or die "File error: $!";
while ($line=<DATA>) {
if ($line =~ /$gene/) {
($probe_id) = split(/\s/,$line,2);
print "$gene\t$probe_id\t$genedex{$gene}\n";
}
}
Hope that helps you along.
James
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