Solved

$variable passing

Posted on 2009-05-10
7
137 Views
Last Modified: 2012-05-06
Hi,
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.
0
Comment
Question by:StephenMcGowan
  • 3
  • 3
7 Comments
 
LVL 48

Expert Comment

by:Tintin
Comment Utility
How are you calling proteindigest.pl?

0
 
LVL 84

Expert Comment

by:ozo
Comment Utility
Do you get to write proteindigest.pl?
If not, how does it currently like to receive variables?
0
 

Author Comment

by:StephenMcGowan
Comment Utility
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?
0
How to run any project with ease

Manage projects of all sizes how you want. Great for personal to-do lists, project milestones, team priorities and launch plans.
- Combine task lists, docs, spreadsheets, and chat in one
- View and edit from mobile/offline
- Cut down on emails

 
LVL 84

Accepted Solution

by:
ozo earned 50 total points
Comment Utility
if proteindigest.pl starts with
my($var1,$var2,$var3,$var4,$var5,$var6)=@ARGV;

then you can call
system 'proteindigest.pl', $var1,$var2,$var3,$var4,$var5,$var6;
0
 

Author Comment

by:StephenMcGowan
Comment Utility
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

my($longorf1,$longorf2,$longorf3,$longorf4,$longorf5,$longorf6)=@ARGV;

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?
0
 
LVL 84

Expert Comment

by:ozo
Comment Utility
'./proteindigest.pl'
if proteindigest.pl is in the current working directory.
how was ORFfinder.pl invoked?
0
 

Author Comment

by:StephenMcGowan
Comment Utility
Thanks ozo,

It's worked a charm.. I had it as ./'proteindigest.pl'; with ./ outside the quotations.
0

Featured Post

Do You Know the 4 Main Threat Actor Types?

Do you know the main threat actor types? Most attackers fall into one of four categories, each with their own favored tactics, techniques, and procedures.

Join & Write a Comment

On Microsoft Windows, if  when you click or type the name of a .pl file, you get an error "is not recognized as an internal or external command, operable program or batch file", then this means you do not have the .pl file extension associated with …
A year or so back I was asked to have a play with MongoDB; within half an hour I had downloaded (http://www.mongodb.org/downloads),  installed and started the daemon, and had a console window open. After an hour or two of playing at the command …
Explain concepts important to validation of email addresses with regular expressions. Applies to most languages/tools that uses regular expressions. Consider email address RFCs: Look at HTML5 form input element (with type=email) regex pattern: T…
Access reports are powerful and flexible. Learn how to create a query and then a grouped report using the wizard. Modify the report design after the wizard is done to make it look better. There will be another video to explain how to put the final p…

772 members asked questions and received personalized solutions in the past 7 days.

Join the community of 500,000 technology professionals and ask your questions.

Join & Ask a Question

Need Help in Real-Time?

Connect with top rated Experts

16 Experts available now in Live!

Get 1:1 Help Now