Extract rows present in file1 and not in file 2

Question

[biostarsb]

I have two files with genes

File one (with 40000 genes)

Gene 1
Gene 2
Gene 3
Gene b
Gene f
Gene c
Gene r
Gene z

File two (with 39000 genes)

Gene 1
Gene 3
Gene 2
Gene b

I would like to know if there is a command line (with awk or bash) to extract that lines that exist in the one file and not in the two file

Answer 1

[Pierre Lindenbaum]

I would like to know if there is a command line (with awk or bash) to extract that lines that exist in the one file and not in the two file

use comm : http://man7.org/linux/man-pages/man1/comm.1.html

comm -3 <(sort file1.txt)  <(sort file2.txt )

[biostarsb]

i tested this but i have all genes not only those in the file1 me i need to extract only genes present in file1 and not in file2

[Pierre Lindenbaum]

only in 1st:

comm -23 <(sort file1.txt)  <(sort file2.txt )

only in 2nd

comm -13 <(sort file1.txt)  <(sort file2.txt )

Answer 2

[Asaf]

Get all unique genes:

cat file1.tx file2.txt |sort |uniq -c |awk '$1==1'

Get genes in file 1 not in file2:

grep -w -f file2 -v file1

[Pierre Lindenbaum]

use uniq -u instead of uniq -c |awk '$1==1'

Answer 3

[shenwei356]

What not simply use grep?

grep -f file2.txt -v file1.txt

[Pierre Lindenbaum]

• if 'gene2' is in file2.txt it will remove 'gene22' from file1.txt
• in general , if file2.txt is big, you wouldn't want to put this in memory.

[shenwei356]

You're right! Thanks