using strict - ADDENDUM

[Hans Holtan]

Hi everyone,

I forgot to mention that I did open the output files earlier in the 
program, ie CHR1, CHR3 ... CHR5.

Here is the whole thing:


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


my ($input,$output,$k,$v,$gene, $input_string, 
$output1,$output2,$output3,$output4,$output5,
         $file, $junk,$i,
         @temp_list,
         %all_genes);


#open a new text file
$output1 =  ">../perl_output/AtChr1.txt";
open (CHR1, "$output1") or die "Could not open $output1.$!";
$output2 =  ">../perl_output/AtChr2.txt";
open (CHR2, "$output2") or die "Could not open $output2.$!";
$output3 =  ">../perl_output/AtChr3.txt";
open (CHR3, "$output3") or die "Could not open $output3.$!";
$output4 =  ">../perl_output/AtChr4.txt";
open (CHR4, "$output4") or die "Could not open $output4.$!";
$output5 =  ">../perl_output/AtChr5.txt";
open (CHR5, "$output5") or die "Could not open $output5.$!";

#open "AtIntergenicTable.txt"
$input =  "<../perl_output/AtIntergenicTable.txt";
open (INPUT, "$input") or die "Could not open $input.$!";
#read it into memory
while (<INPUT>) {
         next if (/>/);
         $input_string .= $_}
close (INPUT);


#split it into a hash, geting the TAIR anotation as keys and the next 
line as the value
@temp_list = split (/#/, $input_string);
map (chomp, @temp_list);
foreach $gene (@temp_list){
         ($k, $v) = split (/:/, $gene);
         $all_genes {$k} = $v;
         }


#Sort the hash and write to a new file
foreach $k (sort keys (%all_genes)) {
         for (1..5){
                 if ($k =~ /[$_]g/){
                         $file = "CHR$_";
                         print $file ">$k\t$all_genes{$k}\n";
                         last;
                 }
         }
}