Pattern search


 
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# 1  
Old 10-10-2018
Pattern search

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

but didnt get expected result.

Can anyone help?

Last edited by RudiC; 10-10-2018 at 12:04 PM..
# 2  
Old 10-10-2018
a sample input file and a desired output would be a good start (as always).
# 3  
Old 10-10-2018
>my_file
Code:
GTGTGTCATTTTAGCCCGTTGGGTTTCATTAAGGTGTGTCACCAGGTGGGTGGTACCTGGAGGTTATTCT
ATTGGGATAACGAGAGGAGGAGGGGCTAGAGGTCCGCGAGATTTGGGGTAGGCGGAGCCTCAGGAGGGTC
CCCTCCATAGGGTTGAACCAGGAGGGGGAGGATTGGGCTCCGCCCCGATATACCTAGTGGGTGGAGCCTA

Expected output
output
Code:
CGTTGGGTTTCATT 17 30


Last edited by vgersh99; 10-10-2018 at 12:15 PM.. Reason: please start using code tags!
# 4  
Old 10-10-2018
something along these lines:
Code:
awk 'match($0,/CGTTG.*TTCATT/) {print substr($0,RSTART,RLENGTH), RSTART, RSTART+RLENGTH}' myFile

# 5  
Old 10-10-2018
Thanks,

The pattern is also in other positions, I need to get all the positions the pattern matches to.
# 6  
Old 10-10-2018
Quote:
Originally Posted by Ibk
Thanks,

The pattern is also in other positions, I need to get all the positions the pattern matches to.
There's nothing in the suggested solution that assumes any particular "position".
Then please provide a representative sample and desired output.
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