If you haven't been using Data::Dumper yet, now is the time to start... 
use Data::Dumper;  # add this near the top of your script:

# ... now, down at line 383 (had been 382 before adding "use Data::Dum
+per":
       SITEKEY: for $sitekey (sort {$a <=> $b } keys %{$matches{$fasta
+seq}}) {
         print "\$matches{$fastaseq}{$sitekey} is:\n",
               Dumper( $matches{$fastaseq}{$sitekey} ); # add this
         SET: foreach $hit ( ... ) {
           # the above print statement used to be here

[download]
Also, if you haven't started using "perl -d" to run your script, it's time to learn about the perl debugger, so you can step through your code and check what is being assigned to your structure as it happens.

One other hint: if you're looking at data structure trouble at line 384 and you've lost your train of thought, your problem may be "fasta pasta" -- i.e. spaghetti code. (Sorry, couldn't resist.)

Try modularizing -- identify functions or code blocks that can be made fairly independent, put them into separate files that simply define subroutines, and put "require" statements into the main script to load those other files.

This will make it easier to test things, and so long as the different "modules" really function independently, you'll find it easier to focus your attention on the problem areas, because they will be smaller. The discipline of not using or altering global variables within subroutines (because the subs will be defined in separate source files), will do you good.

In reply to Re: foreach in HoHoA problems by graff
in thread foreach in HoHoA problems by mdunnbass

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