How to copy only certain counts for genes in tsv file to new file in linux

Question

Hi there I have generated a counts table of samples I need to compare by differential expression analysis.

The layout of the counts table is as follows:

Gene_id	Sample_A_r1	Sample_A_r2	Sample_B_r1	Sample_B_r2	Sample_AB_r1	Sample_AB_r2
KLTH001	0	0	2	5	8	3
KLTH002	0	0	5	3	9	7
YL99812	6	4	0	0	12	14
YL99813	9	7	0	0	15	19

So here, for the differential expression analysis, I only want to compare for example the genes starting with "YL-". So in a new file I want the rows including the first row which is "Gene_id" and the sample names e.g. "Sample_A_r1" and then only the rows with genes starting with "YL-" in their names. This will allow me to only compare the changes between Sample_A alone versus when it was combined with Sample_B, or in the table Sample_AB.

If anyone can please give me an indication of how to do this in linux I would really appreciate it. I have seen other similar posts, involving grep and awk I am just not sure of exactly how to do this. I am still quite new to linux. Any help will be appreciated.

Answer 1

Something like this should do job:

# creating a new file with the first line of the original    
head -1 foo.txt > bar.txt

# ">>" appends to the file on the right hand side
# "^" dictates that the search term should be at the beginning of a line
grep "^YL" foo.txt >> bar.txt 

Answer 2

One way using awk:

awk 'NR==1 || /^YL/ { print $0 }' file.tsv

The default action is to print the line/record, so all you need is the condition:

awk 'NR==1 || /^YL/' file.tsv

Answer 3

Alternatively, you can use grep like so to remove all lines starting with KLTH:

grep -v '^KLTH' in_file > out_file

For example:

echo "Gene_id\nKLTH001\nYL99812" | grep -v '^KLTH'

Prints:

Gene_id
YL99812

Here, GNU grep uses option:
-v : Print lines that do not match.

In the regular expression (regex):
^ : Match the beginning of the line.