Problem with string comparison ?

[vicky bioinfo]

Hi,

I want extract particular strings from large file(file size 600 Mb). I gave two kind of conditions for identify the position. first string comparison is working, but second one is not working. Please helpm in this. Thanks in advance.

 
open(NGS,"<$ngs") || die "can't open file";
open(RESULT,">$output") || die "can't open file";
 
@ngs_seq = <NGS>;
$NGS_length = @ngs_seq;
      $z=0;
           for($j = 0; $j <= $NGS_length; $j++)
              {
 
            $fastasymbl= substr($ngs_seq[$j], 1, 1);
 
             if($fastasymbl eq '>')#1st working
                 {
 
                    ($a1, $b1, $c1, $d1, $e1, $f1)=split(/\|/, $ngs_seq[$j], 6);
                   #chomp $b1;
                  # $b1=~s/\s//g;
 
                  if($b1 eq 'A 0 1')#2nd not working
                    {
                       print "$b1\n";
                       $z++;
                     }
 
                   }
                }
            print "\n total number of scaffolds: $z\n";
close NGS; 
 

[numberwhun]

To begin to help you, we are going to have to see the contents of the file referenced by $ngs.

Also, one suggestion, when doing a die statement, instead of just saying it couldn't open the file, you might want to tell 'why' it couldn't. I usually write my die statements like this:

open(NGS,"<$ngs") || die "can't open file $ngs: $!";
 

Notice the $!. That will print out the last error that was issued, that way you know what was wrong. Also, I referenced the file you were trying to open ($ngs). That way, since you can potentially have many die statements, you will know 'where' the error took place in the script and what was effected.

Regards,

Jeff

[vicky bioinfo]

Hi numberwhun,


Thanks for ur suggestion. I found the error was with the file only. it was in unicode. After changing to ANSI it's working.

When it was in unicode, looks normal but program reads space between each letter. I don't know why?

[numberwhun]

For your reading enjoyment, go here.


Regards,

Jeff