Saving a file into a hash

[perlybuddy]

Hello.

I have a file named "test.fasta" which contains three patterns and looks like

>1elwA
AAAAAASSSSSSSSSSSSSSDDDDDDDDDDDFFFFFFFFFF
>1flwA
GGGGGGGGGGHHHHHHHHHHHHIIIIIIIIIIIIIIJJJJJJJJJJ
>1ghwA
KKKKKKKKKKLLLLLLLLLLMMMMMMMMMMNNNNNNNNNNOOOOO

I want to store each pattern into hash with the name (>1elwA, >1flwA, >1ghwA, in this case) being the key and the other data being the value of the hash. My code is

#!/usr/bin/perl
my %seqInfo = ();
open(FILE, 'test.fasta');
{
while(<FILE>)
{
my $line = $_;
 if ($line =~ />.*/)
  {
  #print "$&\n";
  }
else
  {
  #print "$line\n";
  }
$seqInfo{$&} = $line;
print "$& => $line\n";
}
}
 

The output is like

 => >1elwA
 
 => AAAAAASSSSSSSSSSSSSSDDDDDDDDDDDFFFFFFFFFF
 
 => >1flwA
 
 => GGGGGGGGGGHHHHHHHHHHHHIIIIIIIIIIIIIIJJJJJJJJJJ
 
 => >1ghwA
 
 => KKKKKKKKKKLLLLLLLLLLMMMMMMMMMMNNNNNNNNNNOOOOO
 

However according to my understanding the output should be like

>1elwA => AAAAAASSSSSSSSSSSSSSDDDDDDDDDDDFFFFFFFFFF
 
 

What modifications are required in my code to get the required output. I am assuming that in this case my keys and values are not being stored properly. Any thoughts?? I shall be very thankful.

[numberwhun]

Ok, here is what I used in the text file:

>1elwA
AAAAAASSSSSSSSSSSSSSDDDDDDDDDDDFFFFFFFFFF
>1flwA
GGGGGGGGGGHHHHHHHHHHHHIIIIIIIIIIIIIIJJJJJJJJJJ
>1ghwA
KKKKKKKKKKLLLLLLLLLLMMMMMMMMMMNNNNNNNNNNOOOOO
 

That has each element on a separate line. So, the trick to this, that I used that is, was counting. You are only ever worried about 2 lines at a time. So, as you will see, I used a counter in this code. I hope this helps:

#!/usr/bin/perl
 
use strict;
use warnings;
 
my %seqInfo;
my $key;
my $val;
my $count = 0;
 
open(FILE, '<file2hash.txt');
 
while(<FILE>){
    my $line = $_;
    chomp($line);
 
    if($count == 0){
        $count++;
 
        if($line =~ m/\>\d.*/){
            $key = $line;
        }
        next;
    }
 
    if($count == 1){
        $count++;
 
        if($line =~ m/\w+/){
            $val = $line;
        }
 
        if($count == 2){
            if($key && $val){
                $seqInfo{$key} = $val;
            }
 
            $key = "";
            $val = "";
            $count = 0;
        }
 
        next;
    }
}        
close(FILE);
 
while( my ($k, $v) = each(%seqInfo)){
        print "key: $k, value: $v.\n";
}
 

I ran it and it seemed to work fine.

Regards,

Jeff

[numberwhun]

Ok, here is what I used in the text file:

>1elwA
AAAAAASSSSSSSSSSSSSSDDDDDDDDDDDFFFFFFFFFF
>1flwA
GGGGGGGGGGHHHHHHHHHHHHIIIIIIIIIIIIIIJJJJJJJJJJ
>1ghwA
KKKKKKKKKKLLLLLLLLLLMMMMMMMMMMNNNNNNNNNNOOOOO
 

That has each element on a separate line. So, the trick to this, that I used that is, was counting. You are only ever worried about 2 lines at a time. So, as you will see, I used a counter in this code. I hope this helps:

#!/usr/bin/perl
 
use strict;
use warnings;
 
my %seqInfo;
my $key;
my $val;
my $count = 0;
 
open(FILE, '<file2hash.txt');
 
while(<FILE>){
    my $line = $_;
    chomp($line);
 
    if($count == 0){
        $count++;
 
        if($line =~ m/\>\d.*/){
            $key = $line;
        }
        next;
    }
 
    if($count == 1){
        $count++;
 
        if($line =~ m/\w+/){
            $val = $line;
        }
 
        if($count == 2){
            if($key && $val){
                $seqInfo{$key} = $val;
            }
 
            $key = "";
            $val = "";
            $count = 0;
        }
 
        next;
    }
}        
close(FILE);
 
while( my ($k, $v) = each(%seqInfo)){
        print "key: $k, value: $v.\n";
}
 

I ran it and it seemed to work fine.

Regards,

Jeff

[perlybuddy]

Thankyou Jeff...it worked :) :)

[numberwhun]

Just so you know, the output when you run my code above is:

./file2hash.pl
key: >1ghwA, value: KKKKKKKKKKLLLLLLLLLLMMMMMMMMMMNNNNNNNNNNOOOOO.
key: >1flwA, value: GGGGGGGGGGHHHHHHHHHHHHIIIIIIIIIIIIIIJJJJJJJJJJ.
key: >1elwA, value: AAAAAASSSSSSSSSSSSSSDDDDDDDDDDDFFFFFFFFFF.

I know that you put something else, but that is configurable and you can change it to however you like.