Hi all
I am too new with programing to solve this problem. I have two files, file1 containing the index, file2 includes information I want.
1. file1
CU_91
CU_495
CW_79
CU_22
CW_42
2. file2
CW_79 protein1
CW_15 protein2
CW_16 protein3
CW_17 protein4
CW_42 protein5
I want to add extra information from file 2 to file 1 without changing the order in file one, as following. How could I do that?
CU_91
CU_495
CW_79 protein1
CU_22
CW_42 protein5
Thank you!
Alexie
•
written
by
Anny •
What you've described is a left-outer-join of the data in file1 with the data in file2. Have a look at the join command (example). If your file2 is tab-separated, I think you do the following:
join -t $'\t' file1 file2 -a1
For example,
echo -e "A\nB\nC" > f1
cat f1
A
B
C
echo -e "A\tP1\nC\tP2\nD\tP3" > f2
cat f2
A P1
C P2
D P3
join -t $'\t' f1 f2 -a1
A P1
B
C P2
The syntax is a bit awkward for specifying the separator IMO
Hi russhh!
Thank you for your help.
I tried this method but failed to get the result, I think there are two problems
1)I can't sort file 1 since I need the order information
2)For some reason, my system is not recognizing "join -t $'\t'" and gave the error message "join: illegal tab character specification". I changed file two with command sed 's/ /\t/g'
assuming the tab is the delimiter. The first awk is used to keep the line number of the first file.
join -t $'\t' -a 1 -1 2 -2 1 \
<(awk '{printf("%d\t%s\n",NR,$1);}' file.1 | sort -t $'\t' -k2,2) \
<(sort -t $'\t' -k1,1 file.2) |\
sort -t $'\t' -k2,2n | cut -f 1,3
CU_91
CU_495
CW_79 protein1
CU_22
CW_42 protein5
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