Thanks iraun. The merger line is perfect.
• 0 views
•
link
written
by
emiliomastriani •
combine headers from two fasta files
Dear all, I am in the following situation. I have two files: 1. it is a collection of sequences in fasta format for emu; 2. the list of sequences with more taxonomic information. Please, find a "fake" example of them:
- genome.txt
> 2591237:ncbi:1 [MK211378]
mammammmammammammammammammammammmammammammammammammammamammammmammammammammammammammammmammammammammammammammamammammmammammammammammammammammmammammammammammammammamammammmammammammammammammammammmammammammammammammammamammammmammammammammammammammammmammammammammammammammamammammmammammammammammammammammmammammammammammammammamammammmammammammammammammammammmammammammammammammammamammammmammammammammammammammammmammammammammammammamma
>11120:ncbi:1011 [MG021194]
banananavananabananabananabanananavananabananabananabanananavananabananabananabanananavananabananabananabanananavananabananabananabanananavananabananabananabanananavananabananabananabanananavananabananabananabanananavananabananabananabanananavananabananabananabanananavananabananabananabanananavananabananabananabanananavananabananabananabanananavananabananabananabanananavananabananabanana
- lista.txt
1120 ncbi 1011 [MG021194] 11120 Infectious bronchitis virus scientific name
1237 ncbi 1 [MK211378] 2591237 Coronavirus BtRs-BetaCoV/YN2018D scientific name
`
What I want to obtain is an "extended" version of the genome.txt file where the header of each sequence has been combined to the information from the lista.txt file. The "join" operation could be done by the sequence ID (already unique, e.g MK211378). I already tried to use the join (bash) command and awk, but without results.
Please, can someone help me?
Thank you very much.
Emilio
• 1,462 views
•
link
updated
by
iraun
•
written
by
emiliomastriani •
•
written
by
emiliomastriani •
1 answer
Hi! Try this and check if it does what you need.
It is not obviously the most elegant work, but maybe you can take it from here and adapt it to your needs.
awk 'FNR==NR{split($0,a,"[");split(a[2],b,"]"); c[b[1]]=$0; next}NR>1{split($0,a,"[");split(a[2],b,"]"); if (b[1] in c) { print $0"\t"c[b[1]]} else {print}}' lista.txt genome.txt
Log in to answer this question.