Trying to get UNIX to read gene names in one file so I can grep lines from another file

Question

[mxm189]

Hi there question is in the title,

I found an article that lists a number of genes, I made a text file out of this, called MTOR. Using MTOR.txt I wanted to use UNIX or a Bash script to read the contents of this list, and then search in a CSV file (SkeletalMuscle) the lines that contain the name of the genes. These lines contain Differential gene expression. I tried using grep and awk separately but honestly I'm kinda new to UNIX, still have to get used to it and I'm at the point where I think to myself maybe I should just try using Excel and using VLOOKUP or something... please help

[GenoMax]

Show the contents of the files in question. A simple head -5 filename should be adequate.

[mxm189]

This is the Simple MTOR text file:

LAMTOR1
LAMTOR2
LAMTOR3
LAMTOR4
LAMTOR5

This is the SkeletalMuscle.csv file:

genename,WT,A1,FDR,AveExpr,P value,htseq-countdata76B1Mus203_2,htseq-countdata76C1Mus218_2,htseq-countdata76E1Mus209_2,htseq-countdata76F1Mus210_2,htseq-countdata76G1Mus211_2,htseq-countdata76B1Mus203_2 CPM,htseq-countdata76C1Mus218_2 CPM,htseq-countdata76E1Mus209_2 CPM,htseq-countdata76F1Mus210_2 CPM,htseq-countdata76G1Mus211_2 CPM
2010010A06RIK,0,-2.12806812,0.371865991,-4.254517526,0.001484291,1,2,0,0,0,0.1,0.104,0,0,0
4930426L09RIK,0,-2.12806812,0.371865991,-4.254517526,0.001484291,1,2,0,0,0,0.1,0.104,0,0,0
4930455G09RIK,0,-2.731721932,0.371865991,-4.010039042,0.000404351,2,3,0,0,0,0.2,0.155,0,0,0
5830444B04RIK,0,-3.226294438,0.371865991,-1.266945299,0.001403814,26,23,3,1,4,2.597,1.191,0.168,0.058,0.201

Answer 1

[Pierre Lindenbaum]

sort both files and use join https://linux.die.net/man/1/join

[mxm189]

I can try this, tomorrow its 23:42 at the moment. Thanks for the tip will update how it went.

[mxm189]

join -1 1 -2 3 -t "," MTORsorted.txt SMsorted.csv > MTORGENE.txt

gives me an error message:

join: SMsorted.csv:3: is not sorted: 0610009E02RIK,0,-0.557568688,0.791414822,-1.504006552,0.329848873,3,12,3,6,6,0.3,0.621,0.168,0.347,0.301

But I checked SMsorted.csv and its alphabetically sorted. Any tips?

Answer 2

[GenoMax]

See this example. data file contains your data from above.

$ more names
LAMTOR1
LAMTOR2
LAMTOR3
4930455G09RIK

$ grep -w -f names data
4930455G09RIK,0,-2.731721932,0.371865991,-4.010039042,0.000404351,2,3,0,0,0,0.2,0.155,0,0,0

[mxm189]

I don't know if I follow but I will try to use this tomorrow morning. My MTOR file did not contain 4930455G09RIK but I see what the output will be. I'll try, will let you know if it worked out. Thanks for the help

[GenoMax]

I added that name to demonstrate how this will work. I assume that your data csv file will contain LAM* names in it.

[mxm189]

I tried

more MTOR.txt

followed by

grep -w -f MTOR.txt SkeletalMuscle.csv

This did not work... I also tried more MTOR.txt and then followed by grep -w -f SkeletalMuscle.csv but then the terminal does nothing.

[mxm189]

I looked up other people with similar questions and they give a similar solution but when I convert it to a file it returns an empty file... why is that?

grep -w -f MTOR.txt SkeletalMuscle.csv > filterMTORgenes.csv

[GenoMax]

Make sure your files are in "unix" format by using dos2unix if they were created on a windows machine.