Read file in array 1

[mama12]

Hi all,
what is the beste script in Perl to read a file (DNA Sequence)in array and mutate this file between 7% and 10 %

 

[fishiface]

At the risk of sounding desperately unfashionable, I think mama2 is being rude to TWB, who has spent many of his Sunday hours trying to be helpful to a stranger. Apart from anything else, mis-spelling his name as "torjan" seems an odd way of indicating appreciation.

mama12: give it a try. You might learn something and, who knows? you might even enjoy it. Coding is an intrinsic part of modern genetics research and you need to put some effort in if you are going to get anywhere: you can't make a satisfying career by merely piggybacking on others.

I hope that the future of genetics lies in more polite hands.

Sincerely,

fish

["]As soon as we started programming, we found to our surprise that it wasn't as easy to get programs right as we had thought. Debugging had to be discovered. I can remember the exact instant when I realized that a large part of my life from then on was going to be spent in finding mistakes in my own programs.["]
--Maur

 

[TrojanWarBlade]

Thanks guys.
What do you all think of the code? Any thoughts?


Trojan.

 

[duncdude]

Yes - i totally agree with shif ;-)

All that code should transcend any language barriers... i would have expected she could be a bit more grateful than that!


Kind Regards
Duncan

 

[rharsh]

The code looks good Trojan. Just a couple thoughts: one thing that I notice is you could implement a hash of arrays (%lookup) in which the keys are each character from $charset, and the values would be an array of the remaining characters. Something like:

my %lookup = map {my $temp = $_; $_, [map {lc} grep {$_ ne $temp} split('', $charset)]} split('', $charset);

Yuck, that's ugly. But it would save at least one substr call per interation and there's no need for a loop to determine the replacement character. Second, using a lookup hash like that would result in 12 (numChars * (numChars-1)) lc() calls, where the code above would result in numberOfStrings * numberOfSubstitutions * numberOfRatios calls to lc().

Using %lookup,

foreach my $index (keys %indexes) {
  my $char = substr($_,$index,1);
  my $newchar;
  do {
    $newchar = substr($charset, rand(4), 1);
  } while ($char eq $newchar);
  substr($_,$index,1) = lc $newchar;
}

can be boiled down to

foreach my $index (keys %indexes) {
      my $char = substr($_,$index,1);
      substr($_,$index,1,$lookup{$char}[int(rand(@{$lookup{$char}}))]);
}

 

[TrojanWarBlade]

Excellent idea. idea.
I like that.


Trojan.

 

[mama12]

Hi torjan,

I did it, the script is working now, i did little changes on it and it is working now,sorry that I did not let u know.

Kind Regards

mama12

 

[duncdude]

mama12

T r o j a n

NOT Torjan


Kind Regards
Duncan

 

[Corwinsw]

typos happens
s/T.*n/Trojan/g

Corwin

 

[duncdude]

this is not a typo. it is someone's name. not difficult to read. Trojan is 6 letters. i make damn sure if i am asking someone a question a) i get their name right & b) i am polite. sorry, i just don't agree with you

... no offence


Kind Regards
Duncan

 

[ProbablyDown]

Torjan deserves 10 stars for that! ;-)

 

[TrojanWarBlade]

Duncs, easy man!
btw: who is Torjan? ;-)


Trojan.

 

[fishiface]

Torjan is top of my MPV list!

shif

["]As soon as we started programming, we found to our surprise that it wasn't as easy to get programs right as we had thought. Debugging had to be discovered. I can remember the exact instant when I realized that a large part of my life from then on was going to be spent in finding mistakes in my own programs.["]
--Maur

 

[duncdude]

lol fish!


Kind Regards
Duncan

 

[TrojanWarBlade]

LOL


Trojan.

 

[KevinADC]

I wish my momma named me Trojan when I was born, even though it's a popular brand of condoms in the USA, it's still a cool name.

 

[TrojanWarBlade]

Lucky I'm in the UK then!
;-)


Trojan.

 

[fishiface]

UK: change name by deed poll - £20 - bargain!

fish (yes, honestly).

["]As soon as we started programming, we found to our surprise that it wasn't as easy to get programs right as we had thought. Debugging had to be discovered. I can remember the exact instant when I realized that a large part of my life from then on was going to be spent in finding mistakes in my own programs.["]
--Maur