Re^4: Comparing array of aligned sequences

Dear JohnGG, Thank you very much for your time and suggestions. It feels good to learn alternate ways to code for the same input. I have another question to ask regarding generating multiple strings from a general rule. I am trying to generate a string of 10 bases based on certain rule:C)2N3(A|G)4-6N7T8(A|T)9(A|T)10 where N could be (A or T or G or C). So according to the above rule, 1st and 2nd position could be a combination of (GG or GC or CG or CC) followed by (A or T or G or C) at position 3 followed by a combination of (AAA or AAG or AGG .. and so on). The thing which I am not able to figure out is do I need to put lot of loops to do it or is there any short way using perl. Thank you for any help or suggestions.

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Re^5: Comparing array of aligned sequences by johngg (Canon) on Jul 14, 2014 at 22:27 UTC
The glob function is your friend :-) $ perl -Mstrict -Mwarnings -E ' my $rule = q{{c,g}} x 2; $rule .= q{{a,t,g,c}}; $rule .= q{{a,g}} x 3; $rule .= q{{a,t,g,c}}; $rule .= q{t}; $rule .= q{{a,t}} x 2; say $rule; say for glob $rule;' {c,g}{c,g}{a,t,g,c}{a,g}{a,g}{a,g}{a,t,g,c}t{a,t}{a,t} ccaaaaataa ccaaaaatat ccaaaaatta ccaaaaattt ccaaaattaa ccaaaattat ccaaaattta ccaaaatttt ccaaaagtaa ccaaaagtat ccaaaagtta ccaaaagttt ccaaaactaa ccaaaactat ... ggcgggatat ggcgggatta ggcgggattt ggcgggttaa ggcgggttat ggcgggttta ggcgggtttt ggcggggtaa ggcggggtat ggcggggtta ggcggggttt ggcgggctaa ggcgggctat ggcgggctta ggcgggcttt $ [download] Hopefully I've understood your rules correctly and this is helpful. Cheers, JohnGG	[reply] [d/l]
Re^6: Comparing array of aligned sequences by perlfan (Parson) on Jul 15, 2014 at 15:43 UTC
Wow. I learn something every day here. Thank you.	[reply]