Pattern search

Shell Programming and Scripting
1

Hi,

Am trying to print all sequence that matches this pattern CGTTGggtTTCATT and their positions in my file but " ggt " can be any nucleotide. The sequence in big letters must match.

I used

awk 'BEGIN{match("CGTTGGGTTTCATT",/(GGT)+/);print RSTART,RLENGTH}' my_file > output

but didnt get expected result.

Can anyone help?

2

a sample input file and a desired output would be a good start (as always).

3

>my_file

GTGTGTCATTTTAGCCCGTTGGGTTTCATTAAGGTGTGTCACCAGGTGGGTGGTACCTGGAGGTTATTCT
ATTGGGATAACGAGAGGAGGAGGGGCTAGAGGTCCGCGAGATTTGGGGTAGGCGGAGCCTCAGGAGGGTC
CCCTCCATAGGGTTGAACCAGGAGGGGGAGGATTGGGCTCCGCCCCGATATACCTAGTGGGTGGAGCCTA

Expected output
output

CGTTGGGTTTCATT 17 30
4

something along these lines:

awk 'match($0,/CGTTG.*TTCATT/) {print substr($0,RSTART,RLENGTH), RSTART, RSTART+RLENGTH}' myFile
5

Thanks,

The pattern is also in other positions, I need to get all the positions the pattern matches to.

6

There's nothing in the suggested solution that assumes any particular "position".
Then please provide a representative sample and desired output.