extracting single column

[Anonymous Monk]

HI all, This is the code that i have used to extract a particular column from text file.

@arr_file=("R25_s_5_seq_18-26_alignment.txt","R20_s_6_seq_18-26_alignm
+ent.txt");
foreach $file in @arr_file
{
open(FILE, $file);
while(defined($line=<FILE>))
{
@arr_words=split(/\s+/,$line);
print FINAL $arr[2];
}
close FILE;
}
close FINAL;

however it is showing some complation errors plz can any one help me out The file looks like
HWUSI-EAS570R_0000:7:1:5348:9121#0/1 + mmu-miR-16-1-3p 8 TTGACTGTGCTGCTGA IIIIIIIIIIIIIIII 0
and i need to extract only "mmu-miR-16-1-3p"/p> part

[moritz]

The solution is to learn Perl, and to understand what you are doing. Seriously, you can't just make up some syntax and hope that perl will magically convert it into a running, correct program.

Check perlsyn or perlintro for the syntax of the foreach loop.

Writing to FINAL (which you've not opened) is going to be disappointing at run time. use warnings; will catch that (see perllexwarn), and please enable use strict; too. See for example RFC: Tutorial: use strict; now what!? for instructions.

[Marshall]

Perhaps...

#!/usr/bin/perl -w
use strict;

my $somepath = "path to write to..";

my @arr_file=("R25_s_5_seq_18-26_alignment.txt",
              "R20_s_6_seq_18-26_alignment.txt");

open (FINAL, '>', $somepath) or 
        die "cannot open $somepath for write $!";
           
foreach my $file (@arr_file)
{
   open (FILE, '<', $file) or die "cannot open $file for reading $!";
   
   while ( my $line=<FILE> )
   {
      my ($important_thing) = (split(/\s+/,$line))[2];
      print FINAL "$important_thing\n";
   }
}

This is actually just a command line grep.
Type "man grep" at the command prompt.

[choroba]

it is showing some complation errors

can u plz show these errrs so we can help u

[Anonymous Monk]

Bareword found where operator expected at Average.pl line 3, near "$file in" (Missing operator before in?)
Array found where operator expected at Average.pl line 3, at end of line (Do you need to predeclare in?)
syntax error at Average.pl line 3, near "$file in "
syntax error at Average.pl line 12, near "}"
Execution of Average.pl aborted due to compilation errors
.