CODEWITHSUNDEEP
awk
user11766958
user11766958

Reputation: 419

Finding sequence in data

I to use awk to find the sequence of pattern in a DNA data but I cannot figure out how to do it. I have a text file "test.tx" which contains a lot of data and I want to be able to match any sequence that starts with ATG and ends with TAA, TGA or TAG and prints them.

for instance, if my text file has data that look like below. I want to find and match all the existing sequence and output as below.

AGACGCCGGAAGGTCCGAACATCGGCCTTATTTCGTCGCTCTCTTGCTTTGCTCGAATAAACGAGTTTGGCTTTATCGAATCTCCGTACCGTAAGGTCGAAAACGGCCGGGTCATTGAGTACGTGAAAGTACAAAATGG
GTCCGCGAATTTTTCGGTTCGTCTCAGCTTTCGCAGTTTATGGATCAGACGAACCCGCTCTCTGAAATTACTCATAAACGCAGGCTCTCGGCGCTCGGGCCCGGCGGACTCTCGCGGGAGCGTGCAGGTTTCGAAGTTC
GGATGATATCGACCATCTCGGCAATCGACGCGTTCGGGCCGTAGGCGAACTGCTCGAAAATCAATTCCGAATCGGGCTTGAGCGAATGGAGCGGGCCATCAAGGAAAAAATGTCTATCCAGCAGGATATGCAAACGACG
AAAGTATGTTTTTCGATCCGCGCCGATTCGACCTCTCAAGAGTCGGAAGGCTTAAATTCAATATCAAAATGGGACGCCCCGAGCGCGACCGTATAGACGATCCGCTGCTTGCGCCGATGGATTTCATCGACGTTGTGAA
ATGAGACCGGGCGATCCGCCGACTGTGCCAACCGCCTACCGGCTTCTGG

Print out matches:
ATGATATCGACCATCTCGGCAATCGACGCGTTCGGGCCGTAG
ATGATATCGACCATCTCGGCAATCGACGCGTTCGGGCCGTAG
ATGTTTTTCGATCCGCGCCGATTCGACCTCTCAAGAGTCGGAAGGCTTAA

I try something like this, but it only display the rows that starts with ATG. it doesn't actually fix my problem

awk '/^AGT/{print $0}' test.txt

Upvotes: 1

Views: 223

Answers (2)

karakfa
karakfa

Reputation: 67507

assuming the records are not spanning multiple lines

$ grep -oP 'ATG.*?T(AA|AG|GA)' file

ATGGATCAGACGAACCCGCTCTCTGA
ATGATATCGACCATCTCGGCAATCGACGCGTTCGGGCCGTAG
ATGTTTTTCGATCCGCGCCGATTCGACCTCTCAAGAGTCGGAAGGCTTAA
ATGGGACGCCCCGAGCGCGACCGTATAG
ATGGATTTCATCGACGTTGTGA

non-greedy match, requires -P switch (to find the first match, not the longest).

Upvotes: 2

RavinderSingh13
RavinderSingh13

Reputation: 133538

Could you please try following.

awk 'match($0,/ATG.*TAA|ATG.*TGA|ATG.*TAG/){print substr($0,RSTART,RLENGTH)}' Input_file

Upvotes: 1

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