Hi haukex, Thanks very much, works perfectly now. I went with

I was using both Strict and Warnings and using the quotes instead of the regex doesn't produce any warnings :D

My apologies about the input data format

Cheers

I went with

next if ($chromosome =~ "chrM");

That works, but personally I wouldn't write it that way, because writing a regex like for example /chrM/ or m{chrM} makes it more visually clear what you want to do (and also allows you to add modifiers).

I was using both Strict and Warnings and using the quotes instead of the regex doesn't produce any warnings

Are you sure? next if ($chromosome = "chrM"); should have given you the warning "Found = in conditional, should be ==". Perhaps you're not enabling warnings correctly?

Update:

My apologies about the input data format

You can edit your posts (please mark updates as such), see How do I change/delete my post?

Sorry,

I meant no warnings were produced at the end result, I got the warning you mentioned initially before using the ~

Cheers

LeBran:

It didn't give you any warnings because the expression $chromosome = /^chrM/ is perfectly fine. It just doesn't do what you want it to. Instead of checking whether $chromosome starts with "chrM", it instead checks whether $_ starts with "chrM", and then sets $chromosome to a true value if it does, and a false value otherwise. Since you're not using $_ while parsing your lines, it never starts with "chrM" and always returns a false value.

It's a common enough mistake that I could see a case being made for "if ($var = /rex/)" generating a warning, as I expect that "if ($var = ($_ =~ /rex/))" is pretty uncommon (at least, when looking at my code).

...roboticus

When your only tool is a hammer, all problems look like your thumb.

Ah, thank you,

So presumably  next if ($_ = /^chrM/); would also be correct?

Cheers

I went with

next if ($chromosome =~ "chrM");

Also note that  $chromosome =~ "chrM" matches if  "chrM" is found anywhere in the  $chromosome string:

c:\@Work\Perl\monks>perl -wMstrict -le
"my $chromosome = 'foo xx chrM yy bar';
 print 'found a chrM' if $chromosome =~ 'chrM';
"
found a chrM
[download]

This is because you no longer anchor the match to the start of the string (as you do in the code in the OP) with the  ^ match anchor regex operator. The match  /^chrM/ would IMHO be better for what you seem to want.

Another point is that the data posted in the OP has a leading space or spaces in some cases. Leading whitespace will cause the  /^chrM/ match to fail. If leading whitespace may be present in real data, I would recommend something along the lines of  /^\s*chrM/ instead.

---

Give a man a fish:  <%-{-{-{-<

Ah ok,

I'm following you, thanks very much :)