I would but it's large, I'll modify the code in the post.

Well it doesn't have to be real live realsize data, it just has to match your regexes, ie

#!/usr/bin/perl --
#~ 2011-09-21-11:45:38PDT by Anonymous Monk
#~ perltidy -csc -otr -opr -ce -nibc -i=4     
use strict;
use warnings;
use autodie; # dies if open/close... fail

Main( @ARGV );
exit( 0 );

sub Main {
    if ( @_ == 1 ) {
        NotDemoMeaningfulName( @_, 'temp', \&DiddleSomeTemp );
    } else {
        Demo();
        print '#' x 33, "\n", Usage();
    }
} ## end sub Main

sub NotDemoMeaningfulName {
    my ( $inputFile, $outputFile, $callBack ) = @_;

    my $flag    = 0;
    my $outMode = '+>';
    open my ($inFh), '<', $inputFile;
    open my ($outFh), $outMode, $outputFile;
    while (<$inFh>) {
        if (/^#/) {
            if ( not $flag ) {
                $flag++;
                close $outFh;
                open $outFh, $outMode, $outputFile;
            } else {
                seek $outFh, 0, 0;
                $callBack->($outFh);
                close $outFh;
                open $outFh, $outMode, $outputFile;
            } ## end else [ if ( not $flag ) ]
        } else {
            print $outFh $_;
        }
    } ## end while (<$inFh>)
    close $inFh;
    close $outFh;
} ## end sub NotDemoMeaningfulName

sub Usage {
    <<"__USAGE__";


$0    
$0    dataFile     
    
    perl ${\__FILE__}    
    perl ${\__FILE__}    dataFile     


__USAGE__
} ## end sub Usage

sub DiddleSomeTemp {
    warn "Hey diddle diddle @_\n";
    my $f = shift;
    warn "#$_" while <$f>;
}

sub Demo {
    my ( $Input, $WantedOutput ) = DemoData();
    my $Output;

    require Test::More;
    NotDemoMeaningfulName(
        $Input,
        \$Output,
        sub {
            Test::More::is( $Output, $WantedOutput->[0],
                ' NotDemoMeaningfulName Works Aas Designed' );
            shift @$WantedOutput;
        },
    );
    Test::More::done_testing();
} ## end sub Demo

sub DemoData {

#~ http://perlmonks.com/?abspart=1;displaytype=displaycode;node_id=927
+193;part=1
    my $One = <<'__One__';
#
A
B
C
#
D
E
F
#
__One__

    my @Two = (

#~ http://perlmonks.com/?abspart=1;displaytype=displaycode;node_id=927
+193;part=2
        <<'__Two__',
A
B
C blah
__Two__

#~ http://perlmonks.com/?abspart=1;displaytype=displaycode;node_id=927
+193;part=3
        <<'__Two__',
D
E
F blah
__Two__

    );
    return \$One, \@Two;
} ## end sub DemoData

__END__
$ perl pm.927193.pl
not ok 1 -  NotDemoMeaningfulName Works Aas Designed
#   Failed test ' NotDemoMeaningfulName Works Aas Designed'
#   at pm.927193.pl line 76.
#          got: 'A
# B
# C
# '
#     expected: 'A
# B
# C blah
# '
not ok 2 -  NotDemoMeaningfulName Works Aas Designed
#   Failed test ' NotDemoMeaningfulName Works Aas Designed'
#   at pm.927193.pl line 76.
#          got: 'D
# E
# F
# '
#     expected: 'D
# E
# F blah
# '
1..2
#################################


pm.927193.pl
pm.927193.pl    dataFile

    perl pm.927193.pl
    perl pm.927193.pl    dataFile


# Looks like you failed 2 tests of 2.
[download]

As you can see, the logic is sound, temp gets overwritten, pretty much what you already have

Note the expected data doesn't match on purpose ;)

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
[download]

Seek was good idea.

My demo program needed seek because I did not want to touch the filesystem, so I used in-memory filehandles, and passed the filehandle around

You don't need to use seek, it does nothing for you

Thanks for replying so quickly. I'm not quite as advanced as you, and I understood most everything, except the following...

 my $outMode = '+>';

Is the +> telling the file to move out? What is the '+' for?

 open my ($outFh), $outMode, $outputFile;

Here, I know you open a filehandle and then there's the $outMode again (+>) and I'm assuming the name of the output file?

 $callBack->($outFh);

I'm just confused here.

 not $flag

I looked this up in perldocs. Does it return true if $flag = 0?

I didn't mean to turn this into a tutoring session, but it would help me out so much if I understood it! You've been a great help so far.Thanks.

'+>' means that you want both read and write access, but note that it clobbers the file first. For a read/write update that doesn't clobber the file first, do '+<', for non-text files mostly. See: open.

If I don't use seek with the last code I posted, it still appends.

If I don't use seek with the last code I posted, it still appends.

Its not that I don't believe you, but that is just not possible :)

What does autodie say?