Shell Programming and Scripting

Hello

I started to learn bash about 1 or 2 weeks, please help me.

I have about 200000 strings like these:

Code:

 ATGCCAGGGGAGCCCAGAAGGTAAAACTTGATCTGAAATGTATGTTTATATATAATTTAGGTAATCAATTGGCATGTGAA

and I need to split each letter to get:

Code:

 A T G C C A G G G G A G C C C A G A A G G T A A A A C T T G A T C T G A A A T G T A T G T T T A T A T A T A A T T T A G G T A A T C A A T T G G C A T G T G A A

I need this because I want to process each letter like a column by awk, in order to get de porcentual frequency of letters in each position. So if you help me with the awk code too, I will appreciate it so much.

Hi.

Does this give an idea? ... cheers, drl

Code:

echo abc | awk -F "" '{ print $2 }'
b

I already had success splinting the strings whit this sed code:

Code:

 sed -e s/A/A\ /g  -e s/T/T\ /g -e s/G/G\ /g -e s/C/C\ /g

But whit

Code:

 awk -F ""

the it seems not necessary split the strings xD
thanks drl

so why do you need to split the string?? Why not process it as is in awk?
You don't need the space to split it.

Because I didn't know it isn't necessary

k so have you done any C programing or 4GL?
So an array of 26 for the counter results. Then we can walk the string in a loop and depending on the value of the char at pointer we increment the array slot for that value. shell will feed the awk script each line 1 at a time.

Does this sound like a solution or do you have another way?

I don't have previous experience programming.
I'm a undergraduate student of Biochemistry and I have to process large genomic databases to accomplish my thesis goals. So, that's why I started to learn Bash few days a go and I'll start to learn Python soon.