Shell Programming and Scripting

So I have two files that I want to put together via hashes and am having a terrible time with syntax. For example:

Code:

File1

A    apple
B    banana
C    citrus

Code:

File2

A    red
B    yellow
C    orange

What I want to enter on the command line is:

Code:

program.pl File1 File2

And have the result print out

Code:

A    apple    red
B    banana    yellow
C    citrus    orange

What I have been trying to write up in Perl, is a program that is basically as follows :

Code:

foreach line in ARGV[0]
    split the line by tabs
    assign key and value

foreach line in ARGV[1]
    split the line by tabs
    assign key and value

for each key from ARGV[0]
    print key, value, ARGV[1](key)

The code that I've been trying to troubleshoot is:

Code:

  1 #!/usr/bin/perl -w
  2 use diagnostics;
  3 use warnings;
  4 
  5 %affyMap = ();
  6 %affyAnnot = ();
  7 @map = <$ARGV[0]>;
  8 @annotation = <$ARGV[1]>;
  9 $line = "";
 10 
 11 foreach $line (@map){
 12         chomp($line);
 13         my($ID,$info) = split(/\t/,$line,2);
 14         $affyMap{$ID} = $info;
 15 }
 16 
 17 foreach $line (@annotation){
 18         chomp($line);
 19         my($ID,$info) = split(/\t/,$line,2);
 20         $affyAnnot{$ID} = $info;
 21 }
 22 
 23 foreach $key (%affyMap){
 24         print "$key\t" . "$affyMap{$key}\t" . "$affyAnnot{$key}\n";
 25         }

However, when I put a print in the while statement, it doesn't seem to be even making a hash at all since it only reports one "print". I suspect the issue is with the way I am passing in variables, but am now stumped.

I have tried replacing the "foreach $line (@map)" with a "while $line ($ARGV[0])" but it still isn't making the hash tables from what I can tell.

Any help or pointers would be awesome. Thanks!

lines 7 and 8 are wrong. The <> operator reads from a filehandle, not a filename. Look up the proper use of @ARGV and while(<>). You can find @ARGV in perlvar.

perlvar - perldoc.perl.org

I'll search though that link and see if I can't make some sense out of it. Lots of documentation goes over my head still. Probably explains why syntax gets me every time. Thanks!

why not use

Code:

join file1 file2

?

I'm under the impression that join will just append line for line? I am trying to use the hash just in case "file 1" doesn't contain all the elements found in "file2".

I'm working with a large data set from which has a matching file with what they are. Instead of going into excel and manually searching for the item from file1 and copying the respective data from file2, I wanted a script to do it for me, if what I'm trying to do makes any sense.

ETA:
LOL At this rate, it might have been faster for me to go though the few hundred ID's and manually serach, copied, and pasted. If I started doing that when I started trying to do this, I might be finished by now. But I want to get this to work since it would be a one time thing. Thanks for the suggestions!

The reason I did not post any code for you is because your question looks like school work.

That's fine and understandable. I read the user agreement that we can't ask you all do our "hw" for us. I have no problem with trying to read up and figure it out, just need some direction on where to look when the Perl help isn't really help. All it was giving me was that I had an unassigned variable?

It's kind of "school work" in that it will ultimately be used for my thesis research. I'm working on my PhD in Molecular and Cellular Biology and our lab has a mouse microarray data set, for which our post doc is currently manually searching though the sets by hand! Background is in bioengineering, so I didn't feel that it was a very efficient method to go data mining. I've put the data though SAMExcel to find the genes from the array which had a 1.4 fold change and have an associated list of affyID's, but need to connect them with the data found in the affyannotation files. I wish Affy would just use the accession numbers so we could look them up on NCBI or MGI directly, but that's the way it is. I'll stop rambling now though. LOL

I'll keep playing with it! Thanks for the help and suggestions!