Re^3: writing array element to a file

So you have a series of lines that look something like this

> 22 GATTGATGCC...
> 2  GATGGATGTG...
> 26 GATGCATGAT...
> 52 GATGATGTGG...
[download]

And in your output file you just want the numbers.

The split we had in the original code splits each line on spaces into the @vettore array. If we only want to print the second element of this array (the number) then we do not need the foreach loop. We can alter our print to directly address the second element of the arrayprint $out "$vettore[1]\n"; (array indexing starts at 0). Here is our new line processing block:

while (my $line=<$in>) { 
    if($line=~/^>/) {     
        my @vettore=split(/\s+/, $line);  
        print $out "$vettore[1]\n"; 
    } 
}
[download]

For fun it can also be done as a one liner. Here I added a bit more checking of the line to ensure it had some GATC characters following the number

perl -nle "if (/^>\s+(\d+)\s+[GATC]+/) {print $1}" rep_set_ass_tax.fna >> seq_id.txt

If you are not on windows you may need to change the two " quotes to ' quotes.

Cheers,
R.

Pereant, qui ante nos nostra dixerunt!

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Re^4: writing array element to a file by francesca1987 (Initiate) on Apr 25, 2013 at 13:22 UTC
Hi R! I modified the script as you suggested, while (my $line=<$in>) { if($line=~/^>/) { my @vettore=split(/\s+/, $line); print $out "$vettore1\n"; } } but the output file only contained 0, which is the number of the first line. What's I did wrong?	[reply]
Re^5: writing array element to a file by Random_Walk (Prior) on Apr 25, 2013 at 14:31 UTC
It looks like you missed the square brackets around the array index in the print line. `print $out "vettore1\n"; # bad print $out "vettore[1]\n; # good` [download] Cheers, R. Pereant, qui ante nos nostra dixerunt!	[reply] [d/l]
Re^6: writing array element to a file by francesca1987 (Initiate) on Apr 25, 2013 at 14:38 UTC
It wasn't the problem, brakets were there! `my $infile = "rep_set_ass_tax.fna"; my $outfile = "seq_id.txt"; open my $in, '<', $infile or die "Can't read $infile; $!\n"; open my $out, '>>', $outfile or die "Can't read $outfile; $!\n"; while (my $line=<$in>) { if($line=~/^>/) { my @vettore=split(/\s+/, $line); print $out "$vettore[1]\n"; } }` [download]	[reply] [d/l]