my $name = "file000";
open STDOUT, ">>file000" or die "cannot append to file000: $!";
while (<>) {
  if (/Experiment/) {
    open STDOUT, ">>".(++$name) or die "Cannot append to $name: $!";
  }
  print;
  if (/Reagent Lot/) {
    open STDOUT, ">>file000" or die "Cannot re-append to file000: $!";
  }
}
[download]

Will that do, or are there other secret requirements? {grin}

-- Randal L. Schwartz, Perl hacker

You can increment a string like that? Wow!

From perldoc perlop:

       Auto-increment and Auto-decrement

       "++" and "--" work as in C.  That is, if placed before a
       variable, they increment or decrement the variable before
       returning the value, and if placed after, increment or
       decrement the variable after returning the value.

       The auto-increment operator has a little extra builtin
       magic to it.  If you increment a variable that is numeric,
       or that has ever been used in a numeric context, you get a
       normal increment.  If, however, the variable has been used
       in only string contexts since it was set, and has a value
       that is not the empty string and matches the pattern /^[a-
       zA-Z]*[0-9]*$/, the increment is done as a string,
       preserving each character within its range, with carry:

           print ++($foo = '99');      # prints '100'
           print ++($foo = 'a0');      # prints 'a1'
           print ++($foo = 'Az');      # prints 'Ba'
           print ++($foo = 'zz');      # prints 'aaa'

       The auto-decrement operator is not magical.
[download]

-- Randal L. Schwartz, Perl hacker

# 1. open the file 
open FILEHANDLE, $filename or die $!;

# 2. look for my first repeated block
while( <FILEHANDLE> )
{
    if( /(some-regex-for-the-repeat-block)/ )
    {
# 3. save this first repeated block to a variable (which is best?)
# 4. open the first output file 
        open TEMP, "> $outfile" or die $!;

# 5. write the code to this file and close it 
        print TEMP $1, $/;
        close TEMP or die $!;

# 6. repeat to end of file 
}
[download]

{   # note the {} brackets. This concerns the scope of the next line.
    local $/;  # sets $/ = undef for this block only.
    open FH, $infile or die $!;
    $_ = <FH>; # Reads the entire file into memory.
    close FH or die $!;
    @_ = m/(some-regex-for-the-block)/gm;
}

# now @_ contains an array of matches for the regex.
# write each one to a different file:
my $filenum = 0;
for( @_ )
{
    ++$filenum;
    open FH, ">MATCH$filenum" or die "Failed to open MATCH$filenum, $!
+";
    print FH $_, $/;
    close FH or die $!;
}
[download]

@_ = m/(Experiment.*?Reagent Lot)/gs;

It's unclear how you decide the resulting filenames, though. If you have a base name, and just increment a counter, you could do:

foreach my $block (@_) {
    open(OUTPUT, "$file$i") or do { warn "Can't open file: $!"; next }
+;
    print OUTPUT $block;
    close OUTPUT;
}
[download]

Second, if there are many lines between the starting and ending tokens, or if the input file is large, the regex will be very slow. (It has to backtrack quite a ways.) You might be better off going line-by-line if you're dealing with moderately large data files.

Block 1
Start: Experiment 
End  : Reagent Lot
Size : 10 lines followed by one blank line
Block 2
Start : Algorithm Parameters
End   : FCMax
Size  : 5 lines followed by one blank line
Block 3
Start : Experiment
End   : Pixels
Size  : 8 lines followed by one blank line

I had already thought out a short cut - all blocks are the same size, so I simply needed to know how many experiments there were, say 4, and then count down through each of the blocks as I already know the order and size of each. So some simple addition and division could get me where I needed to be.

What I was pretty clueless about was how to match the first block and somehow write it to an output file, repeat for all the Block 1s, then do the same for all the Block 2, etc. I do want to learn how to do multiple line extractions of text - it is a good general technique and I can use it for other stuff - Thank you!

Now I'll go play with your suggestions...
MadraghRua
yet another biologist hacking perl....