Re: convert ambiguous letters in a DNA sequence to all possible non-ambiguous letters


Perl Monk, Perl Meditation
	PerlMonks

Re: convert ambiguous letters in a DNA sequence to all possible non-ambiguous letters

by BrowserUk (Pope)

on Feb 16, 2013 at 01:29 UTC ( #1018995=note: print w/ replies, xml )

Need Help??

in reply to convert ambiguous letters in a DNA sequence to all possible non-ambiguous letters

For strings with upto say a half a dozen or so wildcards, glob does this quite efficiently:

$in = 'ARGBCTC';;

$in =~ s[[^ACGT]][{A,C,G,T}]g;;

print $in;;
A{A,C,G,T}G{A,C,G,T}CTC

print for glob $in;;
AAGACTC
AAGCCTC
AAGGCTC
AAGTCTC
ACGACTC
ACGCCTC
ACGGCTC
ACGTCTC
AGGACTC
AGGCCTC
AGGGCTC
AGGTCTC
ATGACTC
ATGCCTC
ATGGCTC
ATGTCTC
[download]

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

Comment on Re: convert ambiguous letters in a DNA sequence to all possible non-ambiguous letters Download Code
Re^2: convert ambiguous letters in a DNA sequence to all possible non-ambiguous letters by 7stud (Deacon) on Feb 16, 2013 at 02:55 UTC
Gee whiz. That's clever.	[reply]
Re^2: convert ambiguous letters in a DNA sequence to all possible non-ambiguous letters by lrl1997 (Novice) on Feb 18, 2013 at 23:49 UTC
so smart!!!! Thank you indeed!!!	[reply]

In Section Seekers of Perl Wisdom

Node Status^?

node history
Node Type: note [id://1018995]
help

Chatterbox^?

How do I use this? | Other CB clients

Other Users^?

Others exploiting the Monastery: (7)

As of 2013-05-25 05:29 GMT

Sections^?

Information^?

Find Nodes^?

Leftovers^?

Voting Booth^?

The best material for plates (tableware) is:

Results (518 votes), past polls