UNIX for Dummies Questions & Answers

Hello,

I have two files in this form that consist of three columns, a name (L*contig*), the length (length=**) and the sequence

LT_file.txt
and LU_file.txt

I want to compare every sequence in the first file with every sequence in the second file in order to find matches and I want to write both sequences in another file.

For example, in this example, LTcontig8 is included in LUcontig16 since

LTcontig8 length=20 ccattgaccgtacctgatcg
LUcontig16 length=25 ccattgaccgtacctgatcgaaaat

so I want both of these lines in a separate file.

Thank you in advance,
Felipe

Code:

awk '{print $NF}' LT_file.txt | grep -f - LU_file.txt

Code:

awk '{print $NF}' LT_file.txt | while read a
do
grep $a LU_file.txt && grep $a LT_file.txt
done

Thank you very much, it works fine!
So you used "a" as a temporary name for the last column of the file you read with awk?

Yep,
For every line awk takes the last field and give it to the pipe.
for every entry that is passed to the pipe i read it and store it in the "a" variable (of course you could have chosen another name for it).

Also, I have a huge question about the while-loops.
In the code you gave me, if I want to fine how many matches it finds, I tried having an increasing variable inside my loop, but this does not work. I wrote this:

Code:

let h=0;awk '{print $NF}' LT_file.txt | while read a
do
grep $a LU_file.txt && grep $a LT_file.txt
h=$h+1
done

but the variable (h) does not grow inside the loop...

maybe you can try

Code:

let h=0;awk '{print $NF}' LT_file.txt | while read a
do
grep $a LU_file.txt && grep $a LT_file.txt && h=$(($h+1))
done