Substitution

[Vishal G]

Hi Guys,

A Simple Substitution Problem

my $dna =
"***********acgtgcta*****atctgat******actgtaaa***tttt**cccc******ccccc******";

# I want to replace asterisk(*) with dot(.) if 10 or more
asterisks occur together

$dna =~ s/\*{10,}/./g;

print "$dna\n";

# output

.acgtgcta*****atctgat******actgtaaa***tttt**cccc******ccccc******

As you can see 10 or more asterisk are replaced with dot but what
I want is this

...........acgtgcta*****atctgat******actgtaaa***tttt**cccc******ccccc******


How to do it

Vishal

 

[xiechao]

$dna=~s/\*{10,}/"." x length($&)/eg;

 

[Tim Greer]

Hi Guys,

A Simple Substitution Problem

my $dna =
"***********acgtgcta*****atctgat******actgtaaa***tttt**cccc******ccccc******";

# I want to replace asterisk(*) with dot(.) if 10 or more
asterisks occur together

$dna =~ s/\*{10,}/./g;

print "$dna\n";

# output

.acgtgcta*****atctgat******actgtaaa***tttt**cccc******ccccc******

As you can see 10 or more asterisk are replaced with dot but what
I want is this

...........acgtgcta*****atctgat******actgtaaa***tttt**cccc******ccccc******


How to do it

Vishal

Here's one way, off the top of my head:

$dna =~ s/(\*{10,})/'.' x length($1)/eg;

It replaces 10 (or more) instances of \* with ., based on the actual
length of the (\*{10,}) match, replacing each one, with no fixed length
limit (so long as there are 10 or more instances). Just sticking with
your original regex substitution example solution.

 

[Uri Guttman]

x> $dna=~s/\*{10,}/"." x length($&)/eg;

don't use $& as it will slow down all the other regexes in your
program. this is a known problem and trivial to get around. just
explicitly grab the matched string and refer to it with $1


$dna =~ s/(\*{10,})/ '.' x length($1) /eg;

uri

 

[sln]

Hi Guys,

A Simple Substitution Problem

my $dna =
"***********acgtgcta*****atctgat******actgtaaa***tttt**cccc******ccccc******";

# I want to replace asterisk(*) with dot(.) if 10 or more
asterisks occur together

$dna =~ s/\*{10,}/./g;

print "$dna\n";

# output

.acgtgcta*****atctgat******actgtaaa***tttt**cccc******ccccc******

As you can see 10 or more asterisk are replaced with dot but what
I want is this

...........acgtgcta*****atctgat******actgtaaa***tttt**cccc******ccccc******


How to do it

Vishal

So you wan't 5,000,000 asterisks replaced with 5,000,000 dots?
Why?

sln

 

[Rocco Caputo]

my $dna =
"***********acgtgcta*****atctgat******actgtaaa***tttt**cccc******ccccc******";

You seem to be working with genomes. Have you looked at bioperl?
http://www.bioperl.org/wiki/Main_Page

I don't know whether it will solve your problem, but I suspect it may.