in reply to writing array element to a file

Welcome to Perl Monks.

The syntax problem with your code is that foreach runs a loop so you need to use it like this: 

foreach (@vettore) { 
   print $_ . "\n";        
}

[download]

But it looks like you may actually want to print the output to your filehandle $fh by replacing your print with print $fh "$_\n"

Perhaps this script will help show some other ideas

# The following two lines check your code and
# alert you to many common errors
use strict;
use warnings;

# Lets keep the filespec out the main code
# using my when defining a variable limits its scope. 
my $infile  = "rep_set_ass_tax.fna"; 
my $outfile = "seq_id.txt"; 

# No point going on if we can not open both files
# You were opening the outfile in a loop before, lots of opens
# and closes happening that were not needed
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=~/^>/) {           # ^ added for only lines starting with 
+> 
      my @vettore=split(/\s+/, $line);  
      foreach (@vettore) {    # can use for(@array) but they are the s
+ame
         print $out "$_ \n"; # Variables can be interpolated in a stri
+ng
      }                       # end foreach loop    
   } 
} 
close $in;
close $out;

[download]

If you are going to post more often it may be worth having a look at how to format your posts :)

Cheers,
R.

Pereant, qui ante nos nostra dixerunt!

Replies are listed 'Best First'.
Re^2: writing array element to a file
by francesca1987 (Initiate) on Apr 25, 2013 at 11:17 UTC
    Hi! Thanks everyone for the help, I know I did a lot of stupid errors, but I just started with perl. I tried to run the script you suggested me, but it wasn't exactly what I need to do. I need to copy in the stdout only the number after the >, without the following lines. These are few lines of my input file: 
    > 0 
CATCAAAATAATCATGTATTGGTAAAAGTTTAGTAAAAATACTAAAACTATTGACAATTCAAACTAATAC
+TTGTATAATGGAAGCGTATTCAAAAAATAAACAGGAGGTTCTCATAATGAGAAAATCTAACGTTCAGAT
+GAAGTCTCGTCTATCCTATGCAGCGGGTGCTTTTGGTAACGACGTCTTCTATGCAACGTTGTCAACATA
+CTTTATT
> 1 
CATCAAAATAATCATGTATTAGTAAAAGTTTAGTAAAAAATACTAAAACTATTGACAATTCAAACTAATA
+CTTGTATAATGGAAGCGTATTCAAAAAATAACAGGAGGTTCTCATAATGAGAAAATCTAACGTTCAGAT
+GAAGTCTCGTCTATCCTATGCAGCGGGTGCTTTTGGTAACGACGTCTACTATGCAACGTTGTCAACATA
+CTTTATT
> 10 
CATCAAGATAACCATGTATTAGTAAAATTTTAGTAAAAAACACTGAAATTATTGACTGCATAAACCAATT
+TTCATATAATGTAAACGTATTCAAATAATAGGAGGTTTCCGAAATGGAAAAATCTAAAGGTCAGATGAA
+GTCTCGTTTATCCTACGCAGCTGGTGCTTTTGATAACGACGTCTTCTATGCAACCTTGTCAACATTACT
+TTATC
> 100 
CATCAAAATAATCATGTATTAGTAAAAGTTTAGTAAAAATACTAAAACTATTGACAATTCAAACTAATAC
+TTGTATAATGGAAGCGTATTCAAAAAATGACAGGAGGTTCTCATAATGAGAAAATCTAACGTTCAGATG
+AAGTCTCGTCTATCCTATGCAGCGGGTGCTTTTGGTAACGACGTCTTCTATGCAACGTTGTCAACATAC
+TTTATT
...

    [download]
    I want to copy only the numers.... Running the sipt you suggested, I obtained this: 
    > 
0 
CATCAAAATAATCATGTATTGGTAAAAGTTTAGTAAAAATACTAAAACTATTGACAATTCAAACTAATAC
+TTGTATAATGGAAGCGTATTCAAAAAATAAACAGGAGGTTCTCATAATGAGAAAATCTAACGTTCAGAT
+GAAGTCTCGTCTATCCTATGCAGCGGGTGCTTTTGGTAACGACGTCTTCTATGCAACGTTGTCAACATA
+CTTTATT 
> 
1 
CATCAAAATAATCATGTATTAGTAAAAGTTTAGTAAAAAATACTAAAACTATTGACAATTCAAACTAATA
+CTTGTATAATGGAAGCGTATTCAAAAAATAACAGGAGGTTCTCATAATGAGAAAATCTAACGTTCAGAT
+GAAGTCTCGTCTATCCTATGCAGCGGGTGCTTTTGGTAACGACGTCTACTATGCAACGTTGTCAACATA
+CTTTATT

    [download]
    How can I modify it? Man thanks for your help!! Francesca
[reply]
[d/l]
[select]

      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!
[reply]
[d/l]
[select]
        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]

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