#!/usr/bin/perl5.8.8

use strict;
use warnings;
#use autodie; dies if open/close...fail 

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;
open (my $TEMPfa,">",'temp');

while(<$INFILE>)
{
		if ($_ =~/^##UniRef90_([\w\d]+) Protein Family/)
		{
		close ($TEMPfa);
		open ($TEMPfa,">",'temp');
		seek $TEMPfa, 0 ,0;
		}

		if ($_ =~/^>UniRef90_[\w\d]+\.UniRef100_[\w\d]+/ || $_ =~/^[\w\d]+/)
		{
		chomp $_;
		print $TEMPfa "$_\n"; 
		}

		if ($_ =~/^>File/)
		{
		close ($TEMPfa);
		}

} #end of while loop
close ($INFILE); #closes the $INFILE handle
} #end of subroutine tempProteinFamFileCreator