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How do I count strings on each line?

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# 1  
Old 01-27-2013
How do I count strings on each line?
Hi

Im a very inexperienced bioinformatician

I have a large DNA file with about 10000 lines of sequence and need to count the occurrence of TA for each line

for example in the file

Code:
TACGCGCGATA
TATATATA
GGCGCGTATA

I would like to get an output like:

Code:
2
4
2

I have tried various grep and awk commands but can only get total number of TA in the whole file

many thanks
Last edited by Scrutinizer; 01-27-2013 at 02:40 PM.. Reason: code tags
# 2  
Old 01-27-2013
Try
Code:
$ awk '{print gsub("TA","TA")}' file
2
4
2

If you want it a bit more flexible, use a variable like
Code:
$ awk '{print gsub(X,X)}' X="TA" file

This User Gave Thanks to RudiC For This Post:
Manchesterpaul
# 3  
Old 01-27-2013
works perfectly - many thanks!
# 4  
Old 01-27-2013
Alternative:
Code:
awk -F TA '{print NF-1}' file

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