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Run perl script on files in multiple directories


 
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# 1  
Old 06-24-2010
Run perl script on files in multiple directories

Hi,

I want to run a Perl script on multiple files, with same name ("Data.txt") but in different directories (eg : 2010_06_09_A/Data.txt, 2010_06_09_B/Data.txt).

I know how to run this perl script on files in the same directory like:

Code:
for $i in *.txt
do
perl myscript.pl $i > $i.new
done

But my filenames are same, and they are in different directories. How to go about this? This may be a very basic question, but I am just a beginner!!!

Thanks!
# 2  
Old 06-24-2010
Simply pass full/relative paths with directory name to your perl script. (This is assuming your perl script does not expect the file to be in the current working directory).

Code:
## Assuming the following directory structure:
## /abc/xyz/2010_06_09_A
## /abc/xyz/2010_06_09_B
## ...
## /abc/xyz/2010_06_09_Z

cd /abc/xyz
for i in */Data.txt
do
  perl myscript.pl $i > $i.new
done

If your perl script needs the file to be current working directory:

Code:
cd /abc/xyz
for i in */Data.txt
do
  dir=${i%/*}
  file=${i##*/}
  cd "$dir"
  perl myscript.pl ${file} > $i.new
  cd -
done


Last edited by a_programmer; 06-25-2010 at 12:13 PM.. Reason: typo correction: changed for $i to for i
This User Gave Thanks to a_programmer For This Post:
# 3  
Old 06-24-2010
Quote:
Originally Posted by ad23
...
I want to run a Perl script on multiple files, with same name ("Data.txt") but in different directories (eg : 2010_06_09_A/Data.txt, 2010_06_09_B/Data.txt).

I know how to run this perl script on files in the same directory like:

Code:
for $i in *.txt
do
perl myscript.pl $i > $i.new
done

But my filenames are same, and they are in different directories. How to go about this?
...
.... <Shell script snipped> ...
a_programmer's shell for loop is far better.

Perl globbing example follows -

You can iterate through all files named "Data.txt" in the Perl program itself, thereby avoiding the shell's for loop.

Example of your Perl script "myscript.pl" -

Code:
#!/usr/bin/perl -w
...
while ($file = glob("<your_directory>/*/Data.txt")) {
  # Now you have the full path in $file.
  # Process it the way you want.
  # You can even create and write to "$file.new" thereby 
  # avoiding the shell's redirection operator.
  ... your code here
}

HTH,
tyler_durden
This User Gave Thanks to durden_tyler For This Post:
# 4  
Old 06-25-2010
Question

I tried running the script according to a_programmer's code, but it is now giving me an error saying:
Code:
./myScript.sh: $i: is not an identifier

The following is my code:

Code:
#!/bin/tcsh
cd /abc/xyz
for $i in */Data.txt
do
    perl myScript.pl $i > $i.new
done

Am I overlooking something obvious in this?
Thanks again!
# 5  
Old 06-25-2010
Quote:
Originally Posted by ad23
I tried running the script according to a_programmer's code, but it is now giving me an error saying:
Code:
./myScript.sh: $i: is not an identifier

The following is my code:

Code:
#!/bin/tcsh
cd /abc/xyz
for $i in */Data.txt
do
    perl myScript.pl $i > $i.new
done

Am I overlooking something obvious in this?
Thanks again!
Remove the "$" sign and try
This User Gave Thanks to panyam For This Post:
# 6  
Old 06-25-2010
Quote:
Originally Posted by ad23
...
Code:
./myScript.sh: $i: is not an identifier

The following is my code:

Code:
#!/bin/tcsh
cd /abc/xyz
for $i in */Data.txt
do
    perl myScript.pl $i > $i.new
done

Am I overlooking something obvious in this?
...
Yes, you are. $i is a Perl variable; not a shell variable.

tyler_durden
# 7  
Old 06-25-2010
I am still not getting the desired output. Moreover when I print $i it is:

Code:
*/Data.txt

It is not taking the entire path for the file ?
What may be wrong?

---------- Post updated at 11:12 AM ---------- Previous update was at 11:11 AM ----------

When I run this :

Code:
cd abc/xyz

for i in */Data.txt
do
    #echo $i
    perl myScript.pl $i > $i.output
done

I get this error:
Code:
./yourScript.sh: line 10: */Data.txt.output: No such file or directory

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