Data Variable problem. (could somebody have a look at this asap if possible please?)

My programme consists a HTML form, two scripts and two modules. My problem is that I can input data from my HTML form to first script fine, it's just that when i try progressing to the second script i get receive the errors:

Software error:
Unknown enzyme selection ''

Content-type: text/html
Software error:
ran out of frames

Now... these errors occur when the mass.pl button is pressed to send the user over to mass.pl.

Software error:
Unknown enzyme selection ''

Is an option in Script 1, and it is this option which generates the first set of data for the first HTML page. Why this error has been brought up again when going across to the second script is beyond me.

Content-type: text/html
Software error:
ran out of frames

suggests to me that none of my variable data from Script1 has been brought across to Script2 and so a second HTML page isn't generated.

Any help on this would be much appreciated!
DNALib.txt
mass.txt
ORFfinder.txt
ReadingFrameModules.txt
Script1.txt
StephenMcGowanAsked:
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Todd MummertConnect With a Mentor Commented:

The array @fragments is never being populated.  

Your call:
   system './ORFfinder.pl', @fragments, $orfprotein1,$orfprotein2,$orfprotein3,$orfprotein4,$orfprotein5,$orfprotein6;

is running ORFfinder.pl in a separate process... and not populating @fragments.

Furthermore, this statement:
     $orfprotein1,$orfprotein2,$orfprotein3,$orfprotein4,$orfprotein5,$orfprotein6,@fragments='';

is making the problem worse.  All it's doing is making $fragments[0] = ''.     Therefore, there is now a fragment (albeit not a valid one), and you enter the loop that matches fragments to frames.   However,   all of $orfproteinN  are undefined so you get the error message you're seeing above when it tries to compare the fragment against a new frame.




 
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StephenMcGowanAuthor Commented:
Thanks Climbgunks, i think it's getting somewhere,

Is there anyway of re-initialising a variable in a second script?

I've #'d out all the:

system './ORFfinder.pl', @fragments, $orfprotein1,$orfprotein2,$orfprotein3,$orfprotein4,$orfprotein5,$orfprotein6;

$orfprotein1,$orfprotein2,$orfprotein3,$orfprotein4,$orfprotein5,$orfprotein6,@fragments='';

But i'm receiving the errors:

Global symbol "$orfprotein1" requires explicit package name at /home/march09/campus12sm/public_html/Submission/mass.pl line 81.
Global symbol "$orfprotein2" requires explicit package name at /home/march09/campus12sm/public_html/Submission/mass.pl line 81.
Global symbol "$orfprotein3" requires explicit package name at /home/march09/campus12sm/public_html/Submission/mass.pl line 81.
Global symbol "$orfprotein4" requires explicit package name at /home/march09/campus12sm/public_html/Submission/mass.pl line 81.
Global symbol "$orfprotein5" requires explicit package name at /home/march09/campus12sm/public_html/Submission/mass.pl line 81.
Global symbol "$orfprotein6" requires explicit package name at /home/march09/campus12sm/public_html/Submission/mass.pl line 81.
Global symbol "@fragments" requires explicit package name at /home/march09/campus12sm/public_html/Submission/mass.pl line 88.

Is there anyway of reinitialising the variables? or making them universal between two separate scripts? Thanks so much for your time, and for getting back to me!

I think this is the problem!

Stephen

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