in reply to Re: Why is the following instance of Matching using an array element not working
in thread Why is the following instance of Matching using an array element not working

Thanks a lot for this post. I went back and checked

Here is what the contents of the error file look like 
**************************************
Errors for file: Merged_CSVfiles_1.txt
**************************************

Sample_identifier 11SS00342 / IRD Clinic  clinic_HIV000140180:
*  The following fields contain invalid values: Blah blah blah blah
*
Sample_identifier 11SS00336 / IRD Clinic  clinic_HIV000140174:
*  The following fields contain invalid values: Yada yada yada
*
Sample_identifier 11SS00303 / IRD Clinic  clinic_HIV000140141:
*  The following fields contain invalid values: yeah yeah yeah

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Just to check that the array @sample_ids contains the actual ids I printed the contents of the sample id' and got the following 
                    
    push(@sample_ids,$line);
        print(@sample_ids);

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I get the following output which is the list of the ID's (this is just a truncated list, just 8 of the 438 errors) UCD11-02580-V UCD11-02581-P UCD11-02581-V UCD11-02583-P UCD11-02583-V UCD11-02584-P UCD11-02584-V UCD11-02585-P I also did the following as a check 
                    
push(@sample_ids,$line);
                        
    }# End of the if loop
}#End of the for-each loop        

print $sample_ids[3];

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and I got: 11SS00304

What I did realized though was that: 
foreach my $records (@merged_array) {
    my @elements = split /,/, $records;

        print $elements[0];

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The Output from this was: "John Doe"John Doe"John Doe"John Doe"John Doe

I realized that some of the fields themselves had commas within and that I couldn't consistently get the field I wanted by "print18" in this case

Replies are listed 'Best First'.
Re^3: Why is the following instance of Matching using an array element not working
by Kenosis (Priest) on Aug 10, 2012 at 20:31 UTC

    You're most welcome, MyJeweledPerls!

    If getting the field you want from the cvs lines is still presenting a problem, consider using Text::CSV to open and parse your cvs file. Its documentation shows how to do this, so you can get that field.

[reply]

      I have worked with Text::CSV in the past. I have only slight issue with it, which I am not sure if I am not getting how to use it correctly. Here is the following code: 

      my $csv = Text::CSV->new();

open (CSV,"<", "Merged_CSVfiles.csv") || die "File not found\n"; 

    while (<CSV>) {            # While Loop Open Bracket

        next if ($. == 1);
        
        if ($csv->parse($_)) {        #If Open Bracket
        
            my @columns = $csv->fields();
                
                #__ Assigning $columns[0]-$columns[26] to variables
                

                    
                    my @Sample_Ids_m = $columns[16];
                    print ($Sample_Ids_m[0]);        
                    
    
        } else {                    # If Closed Bracket
                                            # Else Open Bracket
        
            my $err = $csv-> error_input; 
            print "Failed to parse line: $err";
            
            close CSV;

        } # Closed Else Bracket
    }#Closed While Loop Bracket

      [download]

      All the ID are loaded into the first element of the array @Sample_Ids_m. This would be a problem but arrays can be different lengths and there are no rules current for constructing Sample ID numbers. It is a random sort of thing.

      If there was some uniformity I could use the substr function and a for loop and extract our individual id's but I dont seem to be able too. I will play around with it for a bit more

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[d/l]

        The script below is based upon the Text::CSV documentation:

        use Modern::Perl;
use Text::CSV;

my @Sample_Ids_m;
my $csv = Text::CSV->new( { binary => 1 } )    # should set binary att
+ribute.
  or die "Cannot use CSV: " . Text::CSV->error_diag();


while ( my $row = $csv->getline(*DATA) ) {
    push @Sample_Ids_m, $row->[6];            # Element 6 is the ID
}

say for @Sample_Ids_m;                         # Print the collected I
+Ds

__DATA__
John Doe,G building,05-Aug-2012,08-Aug-2012,"New York City, NY",ABC234
+5,UCD23467, 
John Moe,H building,05-Aug-2012,08-Aug-2012,New York City,DEF2345,UCD8
+0645,
John Slo,I building,05-Aug-2012,08-Aug-2012,New York City,GHI2345,UCD7
+6765,
John Hor,j building,05-Aug-2012,08-Aug-2012,New York City,JKL2345,UCD8
+7111,

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        Output:

        UCD23467
UCD80645
UCD76765
UCD87111

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        Adapted for your csv file (untested):

        use Modern::Perl;
use Text::CSV;

my @Sample_Ids_m;
my $csv = Text::CSV->new( { binary => 1 } )    # should set binary att
+ribute.
  or die "Cannot use CSV: " . Text::CSV->error_diag();

open my $fh, "<", "Merged_CSVfiles.csv" or die "Merged_CSVfiles.csv: $
+!";
while ( my $row = $csv->getline($fh) ) {

    push @Sample_Ids_m, $row->[16];            # Element 16 is the ID
}
$csv->eof or $csv->error_diag();
close $fh;

say for @Sample_Ids_m;                         # Print the collected I
+Ds

        [download]

        From your code above, it looks like the ID is the 16th element in @columns, and the $row->[16] notation grabs it after parsing a csv line. See if this may assist your scripting...

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[d/l]
[select]

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