you should really put your code in
<code></code> tags. But from what I can see your code looks like this(more or less):
open in, "rep_set_ass_tax.fna";
while ($line=<in>) {
if($line=~/>/) {
@vettore=split(/\s+/, $line);
open my $fh, ">>seq_id.txt" or die "Cannot open output.txt: $!"; #
+ There is no need to open a file each time you need to print somethin
+g into it if it is the same file. just open it once before the loop a
+nd print to it
foreach (@vettore); # What is a loop and what is a proper way to w
+rite one. So you started a loop and what are you going to do with it(
+I mean variables in the loop)
print $_ . "\n"; # OK, so you want to print something, but where
+ to STDOUT or into a file that you have opened
close my $fh; # again my doesn't have any effect if use strict is
+not called.
}
}
First of all try to use strict and warnings, you will get a lot of info about your errors. Second, you have a some syntax errors(see comments in the above code). I I were you I would do something like this
use strict;
use warnings;
open(IN, "<", "rep_set_ass_tax.fna") or die "Died!!";
open (OUT , ">","seq_id.txt") or die "Cannot open output.txt: $!";
while (my $line=<IN>) {
if($line=~/>/) {
my @vettore=split(" ", $line);
foreach (@vettore){
print OUT $_ . "\n";
}
}
}
close IN;
close OUT;
now this maybe is not exactly what you need to do but it will get you started
Cheers
UPDATE:
use strict;
use warnings;
open(IN, "<", "rep_set_ass_tax.fna") or die "Died!!";
while (my $line=<IN>) {
if($line=~/>(\d+)/) {
print $1 . "\n";
}
}
close IN;
UPDATE 2: Did you manage to get it working?? Also is this a fasta file orreally a one line file "> 1 ATTTAAA..."??? it is a bit strange if it is a one liner. usually those files look like this:
>1
ATGT...
>2
ATGGTGC..
also is there a space between > and 1?
so you did several things wrong down there: it should look like this:
use strict;
use warnings;
my $infile = "rep_set_ass_tax.fna";
my $outfile = "seq_id.txt"; # you need to open this only if writing t
+o a file
open(IN, "<", $infile) or die "Died!!";
while (my $line=<IN>) {
if($line=~/>\s*(\d+)/) {
print $1 . "\n";
}
}
close IN;
and use the code tags like:
<code>
My code;
</code>
baxy