Re^2: Got some problem with read write file

Thank you choroba for your precise answer, I changed my code to this:

#!usr\bin\perl -w
open HUBFILE,"1048_undefined.tsv";
@hub=();
while(my $line = <HUBFILE>){
         while ($line =~ /\d \t (\w+) \t/x) {
        push(@hub,$1);
            }
            }close HUBFILE;
            $L=@hub;
    open OUT,">hubs.txt";
    for($i=0;$i<$L;$i++){
    print OUT "HUB:$hub[$i]\n";
    }
    close OUT;
[download]

and i guess something is wrong with the second "while"

Comment on Re^2: Got some problem with read write file Download Code

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Re^3: Got some problem with read write file by choroba (Cardinal) on Sep 03, 2016 at 21:03 UTC
Why is the second while there? Do you want to find several occurences on the same line? Also, you probably don't want to print all the genes found so far after finding a gene, you want to print them once all of them have been found: `#!/usr/bin/perl use warnings; use strict; open my $HUBFILE, '<', '1048_undefined.tsv' or die $!; my @hubs; while (my $line = <$HUBFILE>) { push @hubs, $1 if $line =~ /\d \t (\w+) \t/x; } close $HUBFILE; open my $OUT, '>', 'hubs.txt' or die $!; for my $hub (@hubs) { print {$OUT} "HUB:$hub\n"; } close $OUT;` [download] Notice I modified some other parts of the code, too: I switched to 3-argument open with lexical filehandles, foreach style loop instead of the C-style one, etc. ($q=q:Sq=~/;[c](.)(.)/;chr(-\|\|-\|5+lengthSq)`"S\|oS2"`map{chr \|+ord }map{substrSq`S_+\|`\|}3E\|-\|`7**2-3:)=~y+S\|`+$1,++print+eval$q,q,a, [download]	[reply] [d/l] [select]
Re^4: Got some problem with read write file by SilverWol (Novice) on Sep 03, 2016 at 21:15 UTC
Thought wrong about the second while, I want to print in the second file a list with all the gene names but it just print only the 1st gene name. I didn't know about the lexical filehandles, thank you!	[reply]
Re^5: Got some problem with read write file by Cow1337killr (Monk) on Sep 03, 2016 at 22:01 UTC
I am not a bioinformatician, but I wanted to learn about bioinformatics. I read Beginning Perl for Bioinformatics. I really enjoyed it. It got me started on understanding bioinformatics. I think you will enjoy it. It explains how to code in Perl by just explaining to biologists: Here is the problem, here is the code to solve the problem, let me explain the code, move on to the next example program. (I got my copy from the library.)	[reply]