Dear PerlMonks, I am am new to Perl and I have been trying to cobble up some scripts for datasets manipulation (for a few hours:-)). I was trying to extract relevent lines from csv file - for numbers it worked great but for columns with strings I kept getting
Use of uniinitialized value in string eq line 59 <ALL>
(one of the input files). But the value was initialized (I mean variable was declared). I guess it must be some really basic mistake, but have no idea whats wrong - please help.

Thank you karpatov

The program should simplify the csv file by removing rows where a value of certain column is not in a subset of possible values.

What the programs does is:
1.read file with a keyID(1st line) and its values=keys(2nd...nth lines)
2. reads a file to be simplified line by line
3. compares values of column whose header equals keyID with keys
4. lines that pass the test are writen to a new file.
My script is as follows:

#! perl -w
use strict;
use warnings;

sub trim($)
{
        my $string = shift;
        $string =~ s/^\s+//;
        $string =~ s/\s+$//;
        return $string;
}

my $forextract = shift; # IDs to be extracted, 1 per row , further inf
+o tab delimited
            #header[0] is matched against header of dtp_all
my $dtp_all = shift;    # csv CANCER60xxx.lis....
my $dtp_my = shift;    # csv output

print "Warning: The file with items to extract has to have a header - 
+the first column name will be matched.\n";
open(IDS,"<$forextract") or die "Opening $forextract failed.\n";
open(ALL, "<$dtp_all") or die "Opening $dtp_all failed.\n";
open(MY, ">$dtp_my") or die "Opening $dtp_my failed.\n";

my @ids_table=<IDS>;
close(IDS);

my $myID="";
my @ids=();
my $count=0;
my $colN=-1;

foreach my $row (@ids_table){
    my @allcolumns = split /\t/, $row;
    if($count==0){$myID= trim($allcolumns[0]);}else{
    $ids[$count] = trim($allcolumns[0]);}
    $count++;
}
# copy the header
my $line = <ALL>;
print MY $line;
my @colnames= split /,/, $line;

my $count2=0;
foreach my $colname (@colnames){
    if($colname eq $myID){$colN = $count2;}
    $count2++;
}
if ($colN ==-1){print "Column $myID not found.\n";
       exit;
}

# parse the input line by line, when ids matched write the line into t
+he output
while ($line = <ALL>) {
    my @columns = split /,/, $line;
    my $NSC = trim($columns[$colN]);
    foreach my $id (@ids) {

       if ($id eq $NSC) {
           print MY $line;
       }
    }
}
close(MY) or die "Not completed $dtp_my\n";
close(ALL);
[download]

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.