#!/usr/bin/perl5.8.8

use strict;
use warnings;

print "Enter file to process\t";
my $count = <>; #captures input from STNDIN and finds the file associated with that number
chomp $count;

tempProteinFamFileCreator(); #creates a temp file with protein family

sub tempProteinFamFileCreator
{
my $infile = $count."_ProFam"; #iterates through all the protein family files with the count variable
open (my $INFILE,"<", $infile);

my $flag = 0;

while(<$INFILE>)
{
my $TEMPfa;	
		if ($_ =~/^#/ && $flag == 0)
		{
		open ($TEMPfa,">",  'temp');
		$flag++;
		}

		if ($_ =~/^[\w\d]+/)
		{
		chomp $_;
		print $TEMPfa "$_\n";
		}

		if (($_ =~/^#/ && $flag == 1) || $_ =~/^>File/) 
		{
		close ($TEMPfa); 
		MuscleHMMERsearch();
		TableParser();
		}	
}
close ($INFILE); #closes the $INFILE handle
} #end of subroutine tempProteinFamFileCreator