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$variable passing

Posted on 2009-05-10
Last Modified: 2012-05-06
Sorry, it's probably a simple, straight forward question, but one i haven't found the answer to yet.

I'm basically trying to pass six variables created from one script "ORFfinder.pl", to another program "proteindigest.pl". I'd assume it'd be a similar method to passing a variable to a subroutine? if it is at all possible?

Thanks in advance.
Question by:StephenMcGowan
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LVL 48

Expert Comment

ID: 24350166
How are you calling proteindigest.pl?

LVL 84

Expert Comment

ID: 24350189
Do you get to write proteindigest.pl?
If not, how does it currently like to receive variables?

Author Comment

ID: 24350212
Hi ozo,

Yeah basically what i'm doing is from the programme i wrote before with the longest dna sequences ($longorf1, $longorf2 etc etc), i'm now trying to pass these to a script "proteindigest.pl" which will then call a sub-routine and convert them from dna to protein sequence before doing some more stuff to the sequences.

If i can't transfer the variables from one script to another i should be ok with creating a sub-routine to carry out the same function. Just not sure if script.pl -> script.pl is possible or not?
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LVL 84

Accepted Solution

ozo earned 50 total points
ID: 24350228
if proteindigest.pl starts with

then you can call
system 'proteindigest.pl', $var1,$var2,$var3,$var4,$var5,$var6;

Author Comment

ID: 24350294
ok, so at the very end of ORFfinder.pl i've put:

system 'proteindigest.pl', $longorf1,$longorf2,$longorf3,$longorf4,$longorf5,$longorf6;

and for proteindigest.pl:

# Initialise variables


but receive the error message:

Can't exec "proteindigest.pl": No such file or directory at ORFfinder.pl line 77.

is there a way of telling it to automatically look in the same directory, if both scripts are in the same directory?
LVL 84

Expert Comment

ID: 24350311
if proteindigest.pl is in the current working directory.
how was ORFfinder.pl invoked?

Author Comment

ID: 24350333
Thanks ozo,

It's worked a charm.. I had it as ./'proteindigest.pl'; with ./ outside the quotations.

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