Awk Assistance - Page 2

jsmithstl · #8 (**permalink**) 6 Days Ago

I see... I think.... A sequence includes all the lines between the headers?

abacus · #9 (**permalink**) 6 Days Ago

Yes,

I think he just needs a count of the sequences that do not contain the letter J. It seems a bit more simpler now.

So a script to read in each sequence and print how many sequences with the letter J.

The example is 1. Due to 1 J sequence.

THanks again for your time and assistance.

Abacus

Scrutinizer · #10 (**permalink**) 6 Days Ago

Something like this then?

Code:

awk '/^>/{if(s==1)t++;s=1;next} /J/{s=0} END{if(s==1)t++;print "J-less sequences: "t}' infile

abacus · #11 (**permalink**) 5 Days Ago

Hmm,
OSX Snow Leopard tested.

Code:

machine1:~ jasonralph$ awk '/^>/{if(s==1)t++;s=1;next} /J/{s=0} END{if(s==1)t++;print "J-less sequences: "t}' infile
J-less sequences: 
c-machine1:~ jasonralph$

Thans for your time as always.

Abacus

ahmad.diab · #12 (**permalink**) 5 Days Ago

you can know the number of sequences that have J on it on each description, then you can grep the zero or write if condition grep the "0" values counter.

Code:-

Code:

gawk '
/^>/{ t=$0 ; a[t]=0 ;next}
/J/{a[t]++  }
END{ for ( i in a ) { printf "J exist in %s sequence(s) of header %s\n",a[i],i } }
'  input_file

Code:

Output

J exist in 2 sequence(s) of header >description 1-blah blah blah
J exist in 1 sequence(s) of header >description 2-blah blah blah

abacus · #13 (**permalink**) 5 Days Ago

Thanks to ahmad.diab, scruitinizer and jsmithstl. The code examples that you have all provided have done the trick.

My friend and I are very satisfied with the level of professionalism found on this site by the users.

Abacus

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Bits Awarded / Charged to jsmithstl for this Post
Date	User	Comment	Amount
5 Days Ago	abacus	Thank you for your assistance...	10,000

Bits Awarded / Charged to Scrutinizer for this Post
Date	User	Comment	Amount
5 Days Ago	abacus	Thank you for your time and expertise....	10,000

Bits Awarded / Charged to ahmad.diab for this Post
Date	User	Comment	Amount
5 Days Ago	abacus	Thank You Sir,	10,000

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