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CSV File parse help in Perl


 
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# 1  
Old 03-29-2008
CSV File parse help in Perl

Folks,

I have a bit of an issue trying to obtain some data from a csv file using PERL. I can sort the file and remove any duplicates leaving only 4 or 5 rows containing data. My problem is that the data contained in the original file contains a lot more columns and when I try ro run this script it finds that all the data is unique.

I have the following fields within the orignal file:
PROGRAM ID,OP,PROBE_CARD ,DEVREVSTEP,TEST_START,TESTER_ID

The data which I need to obtain and sort is within the op,probecard and tester_id fields.

How can I go about this?

The code that I use after manually deleting the fields that i do not require is as follows:

Code:
#!/usr/bin/perl -w
use strict;
my $csvfile = 'probecards.csv';
my $newfile = 'sorted.csv';
my $fieldnames = 1;
open (IN, "<$csvfile")  or die "Couldn't open input CSV file: $!";
open (OUT, ">$newfile") or die "Couldn't open output file: $!";
my $header;
$header = <IN> if $fieldnames;
my @data = sort <IN>;
print OUT $header;
my $n = 0;
my $lastline = '';
foreach my $currentline (@data) {
  next if $currentline eq $lastline;
  print OUT $currentline;
  $lastline = $currentline;
  $n++;
}
close IN; close OUT;
print "Processing complete. In = " . scalar @data . " records, Out = $n records\n";

Sample CSV File:
Code:
Original File:

PROGRAM	ID	OP	PROBE_CARD	DEVREVSTEP	TEST_START	TESTER_ID
12630M196	139	2660	S25E3N36	88BCRA	16/03/2008 12:05	IN01
12630M196	1	2660	S25E3N36	88BLBHD	16/03/2008 13:04	IN04
12630M196	508	2660	S25E3N36	88BCRA	16/03/2008 13:41	IN01
12630M196	437	2660	S25E3N36	88CLNHC	16/03/2008 14:18	IN01
12630M196	465	2660	S25E3N36	88BCRA	16/03/2008 15:34	IN02
12630M196	27	2660	S25E3N36	88BCRA	16/03/2008 18:00	IN01
12630M196	18	2660	S25E3N36	88BCRA	16/03/2008 19:03	IN03


Output:

OPERATION PROBE_CARD_ID	TESTER_ID
2660	S25E3N21	IN04
2660	S25E3N27	IN02
2660	S25E3N36	IN01
2660	S25E3N39	IN03
2660	S25E3N40	IN04

Any pointers on how I could go about this would be greatly appreciated..

Rgds

Colin
# 2  
Old 03-29-2008
That's not a CSV file, it means literally comma-separated values. Traditionally CVS also uses optional double quotes around the values, and then, depending on which wicked version of Excel it's supposed to be incompatible with, more or less insane conventions for values with double quotes in them. Newlines inside a field are also sometimes permitted in CSV.

Is the data you want always in fields 3, 4, and 7?

Code:
cut -f3,4,7 infile

If you require this in Perl, how about

Code:
perl -naF"\t" -e 'print (join ("\t", map { $F[$_] } (2, 3, 6)), "\n")'

# 3  
Old 03-29-2008
I guess the actual problem is that you are comparing the lines before throwing out the fields you don't want to include in the comparison. Before you print, copy the print value to a hash, and if the hash already contains the value, don't print. (Or take the Perl script I gave you and pipe to sort -u -- that's what I would do.)
# 4  
Old 03-29-2008
Where would I put the line in the code?
# 5  
Old 03-29-2008
Code:
cut -f3,4,7 infile | sort -u

That's the whole program.
# 6  
Old 03-29-2008
sorry to be annoying but how does the following perl code work?
Code:
perl -naF"\t" -e 'print (join ("\t", map { $F[$_] } (2, 3, 6)), "\n")'

If i inputed into my code would the { $F[$_] } part need to be made { $F[$csvfile] } ?

I am new to perl so its a learning experience for me Smilie

rgds

colin
# 7  
Old 03-29-2008
That's a somewhat idiosyncratic script, I'm not sure which parts are suitable for a person of your age.

(2, 3, 6) is a list. Map takes the function you give it and applies it to each item on the list in turn, and returns the result as a new list. Within map, $_ refers to the current item. So the map returns $F[2] followed by $F[3] followed by $F[6]. The rest is just formatting.

Oh, the final crucial point is the option -a (mnemonic: more like awk) which says to split the input into @F and, -F "\t" which says to do that splitting on the tab character.

Last edited by era; 03-29-2008 at 03:19 PM..

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