UNIX for Dummies Questions & Answers

Hi,
I have two list I wanna combine and print them together in the output depending if they have the same rsid:
file1:
ENST00000262042 rs47 583 N D
ENST00000408005 rs48 583 N D
ENST00000311322 rs268 318 N S
file 2:
rs34 CHB T 1 C 0 T/T C/T C/C 1 0 0
rs47 JPT T 1 C 0 T/T C/T C/C 1 0 0
rs48 YRI T 1 C 0,017 T/T C/T C/C 1 0 0

output file shold be:
ENST00000262042 rs47 583 N D CHB T 1 C 0 T/T C/T C/C 1 0 0
ENST00000408005 rs48 583 N D JPT T 1 C 0 T/T C/T C/C 1 0 0

can i do it by means of command line*?

thanks for replies

If rsid is the key the given desired output is not correct.

Regards

i have to go through both list and for each line if the rsid is the same eg rs47 i need to print output as shown above

why is CHB part of rs47? that's what franklin is asking you.

ok my mistake, output should be like:
ENST00000262042 rs47 583 N D JPT T 1 C 0 T/T C/T C/C 1 0 0
ENST00000408005 rs48 583 N D YRI T 1 C 0 T/T C/T C/C 1 0 0

if you have Python

Code:

d={}
for line in open("file1"):
    line=line.strip()
    L = line.split()
    d[L[1]] = line
for line in open("file2"):
    line=line.strip().split()
    if d.has_key(line[0]):
        print d[line[0]],' '.join(line[1:])

output

Code:

# ./test.py
ENST00000262042 rs47 583 N D JPT T 1 C 0 T/T C/T C/C 1 0 0
ENST00000408005 rs48 583 N D YRI T 1 C 0,017 T/T C/T C/C 1 0 0

With awk:

Code:

awk '
NR==FNR{a[$1]=$0;sub($1,"",a[$1]);next}
$2 in a{print $0 a[$2]}
' file2 file1

Use nawk or /usr/xpg4/bin/awk on Solaris