Can we please see (simplified) code and sample data. It's hard to know what the problem is from your description. "chomp" should remove whatever is the line end character on your system, but you might be being burned by cross-platform portability issues.

Have you tried something like s/\012|\015//?

Hi again, I'll give a code sample:


#opening the file for reading
  open IN,"$fileName" ;
  #reading the whole file into an array.
  my @F=<IN>; 
  close IN;
  #reading the last line of the file
  my $lastLine=$F[$#F];
  my $firstLine=$F[0];

  #spliting last line by tabs
  my @line=split /\t/,$lastLine;
  #spliting first line by tabs
  my @firstSplitLine=split /\t/,$firstLine;
  #finding the column number that equals the fieldName
  my $fieldNum = -1;
  my $numberOfFields = scalar(@firstSplitLine);
  for($counter=0 ; $counter < $numberOfFields ; $counter++)
  {
    $ourstring = $firstSplitLine[$counter];
    $ourstring =~ s/\n\n/\n/g; #=~ s/ \s//g;# HERE IS WHERE I'M TRYING
+ DIFFERENT STUFF...
     if($fieldName eq $ourstring) # The "problematic" area
     {
    $fieldNum=$counter;
    last;
     }
  }
  # if the field wasn't found
  if($fieldNum==-1)
  {
  print STDERR "\n" if ($permit_writing);
  print STDERR "The field you asked for was not found, now returning l
+ast value: $lastValue\n" if ($permit_writing);
  print STDERR "\n" if ($permit_writing);
  return $lastValue;
  }
  #printing the required field
  print STDERR "    Value: $line[$fieldNum]\n\n" if ($permit_writing);
  return $line[$fieldNum];
[download]

Edit: Changed <pre> tags to <code> tags (davorg)

(Please use <code> tags to display code, not <pre>tags)

Do you have "use warnings" in your code? I ask because the important piece of your code seems to be if($fieldName eq $ourstring) and according to the extract you've shown us, $fieldName is undefined at that point.

But assuming that it's set somewhere outside of this extract, I still think that you can simplify a lot of this code. I'd consider setting up a hash where the keys are the column names and the associated values are the column numbers. Something like:

my %columns;
@columns{@split_first_line} = 0 .. $#split_first_line;
[download]

You can then get the column number associated with a given field name with a simple:

if (defined (my $field_num = $columns{$field_name})) {
  # field exists
}
[download]

Also, the best place to deal with chomping the input data is probably as soon as you've read it in, when a simple chomp(@f) would suffice.

--
<http://dave.org.uk>

"The first rule of Perl club is you do not talk about Perl club."
-- Chip Salzenberg

take a look at $/. Setting that should make chomp work

sed 's/.$//'    # assumes that all lines end with CR/LF
sed 's/^M$//'   # in bash/tcsh, press Ctrl-V then Ctrl-M
[download]

In the quest for a utility to convert between *nix and DOS newlines on a regular basis, I have found flip: Newline conversion between Unix, Macintosh and MS-DOS ASCII files to be useful. It not only converts between DOS and Unix file formats, but also includes a handy -t command-line switch to tell you which format a given file uses.

HTH,