Hello, I have a file containing gene names of interest (24423 genes), and another file containing the lengths to all the genes (41306 genes). I want the lengths only to the 24424 genes, but when I grep using grep -wf file1 file2 or even fgrep -Fwf file1 file2, I get some excess genes, because some genes in my list may contain only the sense or the anti-sense strands, whereas if the reference file may contain both, and that is being reflected.
I want to know if there is a way to remove from the reference file (file2) all the lines that don't match?
Thank you.
P.S. The question is also on stackoverflow.com
edit -
file1
A1BG
A1BG-AS1
TSPAN6
MYB
MYB-AS1
file2
A1BG 2941
A1BG-AS1 560
TSPAN6 7923
MYB-AS1 362
MYB-AS2 713
MYB-AS3 396
desired_output
A1BG 2941
A1BG-AS1 560
TSPAN6 7923
MYB-AS1 362
But I always get MYB-AS2 and MYB-AS3
•
written
by
vinayjrao
2 answers
Hi a simple join would be sufficient:
join file1 file2
It compares the first column of both files. Both files should be in the same order. If they are not, you'll need to sort them : join <(sort file1) <(sort -k1,1 file2)
[EDIT] It works with your example data
this is the correct answer.
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awk extract certain line
written by mxlsherry1992 •
and you'll soon get some negative votes on stackoverflow because you don't show any sample of your files.
Hi, can you post example of your file1, file2 and desire output?