$ while read line; do grep $line test1.txt; done < test2.txt | awk -v OFS="\t" '{print $2,$1}'
Chrysiogenetes 8
Chrysiogenetes 8
Chrysiogenetes 8
Coprothermobacterota 12
Coprothermobacterota 12
Abditibacteriota 13
Abditibacteriota 13
Dictyoglomi 13
Dictyoglomi 13
Rhodothermaeota 36
Rhodothermaeota 36
Join command for the issue
I have a file1 like this
8 Chrysiogenetes
12 Coprothermobacterota
13 Abditibacteriota
13 Dictyoglomi
36 Rhodothermaeota
I have file2 like this
Chrysiogenetes
Chrysiogenetes
Chrysiogenetes
Coprothermobacterota
Coprothermobacterota
Abditibacteriota
Abditibacteriota
Dictyoglomi
Dictyoglomi
Rhodothermaeota
Rhodothermaeota
My expected output:
Chrysiogenetes 8
Chrysiogenetes 8
Chrysiogenetes 8
Coprothermobacterota 12
Coprothermobacterota 12
Abditibacteriota 13
Abditibacteriota 13
Dictyoglomi 13
Dictyoglomi 13
Rhodothermaeota 36
Rhodothermaeota 36
I am using this join command:
join -t $'\t' -1 2 -2 1 <sorted file1.txt> <sorted file2.txt >
but I am not getting expected result because both Abditibacteriota and Dictyoglomi both has "13" so join command is not working properly.
Please help
• 2,650 views
•
link
updated
by
Ram
•
written
by
Confused_human •
•
written
by
Confused_human •
2 answers
It could be better to use grep:
for N in $(cat file2.txt); do grep $N file1.txt | perl -lane 'print "$F[1] $F[0]"' >> out.txt; done
cat out.txt
Chrysiogenetes 8
Chrysiogenetes 8
Chrysiogenetes 8
Coprothermobacterota 12
Coprothermobacterota 12
Abditibacteriota 13
Abditibacteriota 13
Dictyoglomi 13
Dictyoglomi 13
Rhodothermaeota 36
Rhodothermaeota 36
awk -F '\t' 'NR==FNR{a[$1];next} ($2) in a'
awk 'NR==FNR{a[$2]=$1;next}a[$1]{print $0"\t"a[$1]}'
Hi, pls tell me how can I do the same thing using which of this above two commands and if it can be done by modifying any of these commands
• 0 views
•
link
updated
by
Ram
•
written
by
Confused_human •
•
written
by
Confused_human •
Just thought I'd share a more modern and efficient method for joining two CSV files via a common identifier is csvtk - https://github.com/shenwei356/csvtk?tab=readme-ov-file
https://bioinf.shenwei.me/csvtk/usage/#join
I found it a lot easier than trying to use linux sort and join on complex headers.
• 0 views
•
link
written
by
colindaven
Log in to answer this question.
More posts like this
-
awk command merge files on one common column
written by Confused_human •
-
awk command for printing all the repeated matching lines without making them unique
written by Confused_human •
-
How to compare data in two files and print matching data of file1 and file2
written by Kumar
-
How to grep scaffold from the vcf file
written by Kumar
-
GNU parallel command with several multiple arguments
written by FGV
-
Splitting Odd and Even Reads from FastQ to Seperate Output Files
written by landrjos •
-
How to replace row with another row in linux having NA and nucleotide bases
written by Kritika
-
an alternative "join" option for annotated-vcf handling in trios
written by emma.a •
-
Perl :Help to match two IDs from two tables and print to a .txt file
written by rajal2 •
-
Compare one of the columns of two seperate files and write the raw of the second file next to first…
written by emre •
what is the issue and what command you have used to join files?
I have a
file1like thisI have
file2like thisMy expected output:
I am using this join command:
but I am not getting expected result because both Abditibacteriota and Dictyoglomi both has "13" so join command is not working properly.