Thanks Again. Works like I want it too! Seek was good idea. You're pretty brainy. Here's what I ended up using.
#!/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 associa
+ted with that number
chomp $count;
tempProteinFamFileCreator(); #creates a temp file with protein family
sub tempProteinFamFileCreator
{
my $infile = $count."_ProFam"; #iterates through all the protein famil
+y 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