Hello fellow monks!
I have a number of sequences that contain some characters (specifically I,M,O,P,B) and the character U (some times) and I want to get rid of the U's.
There can be these 3 cases:

1. U is in the beginning of the string, like the following example:
$seq=UUUUUUUUIIIIIIIIIIIIIIIMMMMMMMMMMMMMMMMMMMMMMMMOOOOO

[download]

Here, it would be replaced by I, and I do this by writing:
if($seq=~/^(U+)([I|O|P|B|M])/) 
{
 $part_to_change1=$1;
 $len1=length($part_to_change1);
 $char1=$2;
 substr($top, 0, $len1, ($char1 x $len1));             
 }

[download]

2. U is in the end, like the following example: 
$seq=IIIIIIIIIIIIIIIMMMMMMMMMMMMMMMMMMMMMMMMOOOOOUUUUUUUU

[download]

Here, U would be changed to O, and for that I use the following commands:
if($seq=~/.*?([I|O])(U+)$/) 
{ 
  $char2=$1;
  $part_to_change2=$2;
  $len2=length($part_to_change2);
  substr($top, -$len2, $len2, ($char2 x $len2));             
}

[download]

So now, what I am missing is the way to replace U when I find it in the middle of the sequence, like the following examples:
* $seq=IIIIIIIIIIIIIIIMMMMMMMMMMMUUUUUUUUMMMMMMMMMMMMMOOOO
* $seq=IIIIIIIUUUUUIIIIIIIIMMMMMMMMMMMMMMMMMMMMMMMMOOUUUUUUUOO
* $seq=IIIIIIIIIIIIIIIMMMMMMMMMMMMMMMMMMMMMMMMOOUUOO

[download]

In all the above cases, the U needs to be changed to the character that it is 'encapsulated' within, i.e U -> M for the first example, U -> I and U ->O for the second example and U -> O for the third. Can you give me some help?

In reply to Replace characters within string by Anonymous Monk

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