#!/usr/bin/perl
use Cwd;
use strict;
use warnings;

my $path_to_fastaSeqs = $ARGV[0];
my $path_to_fragmentScript = $ARGV[1];
my %seqInfo = ();

&storeInHash;

&createFolderAndFiles;

&callFragmentScript;



sub storeInHash
{
open(FILE, "$path_to_fastaSeqs") or die("cannot open file");
{
while(<FILE>)
{
my $line = $_;
 if ($line =~ />.*/)
  {
  #print "$&\n";
  }
else
  {
  #print "$line\n";
  }
$seqInfo{$&} = $line;
}
close(FILE);
}
}


sub createFolderAndFiles
{
my $dir = getcwd;
while(my ($key, $value) = each(%seqInfo))
{
my $nameWithoutFastaSign = $key;

$nameWithoutFastaSign =~ tr/>//d;

mkdir $nameWithoutFastaSign, 0777;
open(FILEOUT, ">$dir/$nameWithoutFastaSign/$nameWithoutFastaSign.fasta");
{
print FILEOUT "$key\n$value\n";
}
}
}

sub callFragmentScript
{
while(my $key = each %seqInfo)
{
my $nameWithoutFastaSign = $key;
$nameWithoutFastaSign =~ tr/>//d;
my $currentDir = getcwd;
chdir "$currentDir/$nameWithoutFastaSign";
my $changedDir = getcwd;
print "changed directory is: $changedDir\n";

while(my $fastaFile = glob("*.fasta"))
{
print "$fastaFile\n";
}

chdir "$currentDir";

}
}

##</code><code>##

changed directory is: /home/ammarah/Documents/code/1elwA
.fasta
changed directory is: /home/ammarah/Documents/code/1ghwA
.fasta
changed directory is: /home/ammarah/Documents/code/1flwA
.fasta