Hi All,

As been working with awk for a couple of weeks, I've currently come across the problem that I would like to regulate how large my expression is. Below I'll give my example input, code, and desired output

Input: fasta file

>gene445
ATGACACCACTATACCTACACCCCCCCTCTTCAAAATTTTCTACAATACCTTCAAAATTTTCAAAACCATTACCACGTACTCCATTTTCTCTTCAACCCCTTATAAATAAACCCATACCCTTACATAATTACAATTCACTTCAAAATTTTAAATATCATAACCATCTCTACTCTTATTCC
--
>gene450
ATGTTAAAATAACTTCGTTTATCACATCTTCAAAATTTTATGTCTTGCCTTCAAAATTTTACATCATAAACAATCAAGTCATCGACTATTTCCTACTCTTACTAAACACAATCTCTCCACCTCATACACACT
--
>gene455
ATGTTATCTATACATCATTCATTATCATTCCCTTAATTCATCAATCTTCAAAATTTTACTTTTTCTTCAAAATTTTTTCGTACTAACCCAGTACTCTTTCATATCCAAACTATCTGCATAACTTAGATCCTTCAAAATTTTTAAACAGGCACA

Code: awk '/CC*CC/{print $0}' file.fasta

What I would like to regulate is this : CC*CC ; I basically would like to vary the inside of the the brackets CC-[ATCG-of >20]-CC; currently I get all instances of CC-any length-CC; additionally I would like to get the gene added;

Desired output:

>gene445
CCACTATACC   

CCTACACC

CCTCTTCAAAATTTTCTACAATACC  #I would then like to go though each and only filter >20 nt between CC-CC gaps

CCTTCAAAATTTTCAAAACC

CCATTACC

CCACGTACTCC

CCATTTTCTCTTCAACC

CCTTATAAATAAACC

CCATACC

CCTTACATAATTACAATTCACTTCAAAATTTTAAATATCATAACC

CCATCTCTACTCTTATTCC

Perhaps a way to think of what I really want my script to do is the following

1.) open fasta file

2.) identify gene

3.)find the first occurrence of CC

4.) Find the second occurrence of CC

5.) determine length

6.) if length is greater than 20

7.) then add gene# sequence

8.)#4 becomes #3

9.)look for next CC occurrence

10.) repeat step 5-9

11.) complete gene

12.) repeat 2-11

much help appreciated