Compare two files using awk command

[anagari]

Hi all,

I am trying to compare two files and get the output: The files are tab separated.

File1:
chr12 45677 45999 3000 a b
chrX 90999 100000 34 c d

File2:
chr12 45680 46000 300 d g h k
chrY 47800 80000 560 l y z m

I want the all the columns from both files which has:

The first column should be same
2 col of file 1 < 3col in file 2
3col in file 1 > 2col in file 2


I would really appreciate if anyone could help me in this regard ASAP.


Thanks in advance,

PS: I tried to use this command but, didn't understand how to change or modify it for my need:

awk -F"/t" 'NR==FNR{a[$2]=$1FS$3;next} a[$3]{print $0 FS a[$3]}' 2.txt 1.txt > outputfile

[steven]

Hi,
Not sure i got it, but my guess is that you are looking for overlapping intervals.. consider BEDtools.

[gringer]

I'm also not sure what you're asking here. Do you have an example output?

for comparing files side-by-side, 'diff -y' is probably better than awk. If you want to join files on a common field, use 'join'. If you just want to combine files so that one file appears to the left of the other, use 'paste'. [all standard Linux commands]

[Clare S]

Hi anagari,

I don't know if this is the kind of path you want to go down (non command-line) but galaxy (usegalaxy.org) has built-in tools for finding overlapping intervals as well.

You can essentially upload your files and then from the tools on the left select Operate on Genomic Intervals -> Intersect