Bash solution to replace part of FASTA headers witch contain matching values in another file

Question

[clmattson]

Hi all,

this is my first time posting on BioStars! I thought I'd easily find a bash one-liner to take care of this task but I've been searching with no luck.

I have a fasta, samples.fasta, that looks like this:

>sample01/contig002
ATCG
>sample02/contig001
GCTA
>sample11/contig003
CAGT

I have a text file, sample_key.txt, that has samples (always format 'sampleXX') paired with isolate names. Isolate names have a variety of formats, but none of them contain spaces. sample_key.txt looks like this:

sample01     AAA
sample02     def456
sample03     F7
.....
sample11     H-10

I'm trying to do two things: 1) replace the sample name with the isolate name (ie the value in the key file) and 2) replace the '/' in the original header with a '_'. I want to keep the second part of the original header, the contig number. My ideal output, looks like this:

>AAA_contig002
ATCG
>def456_contig001
GCTA
>H-10_contig003
CAGT

I've tried seqkit replace, but it doesnt seem to work unless the keys match the existing headers exactly, which wont be the case here because sample_key.txt only contains part of each header. Unless you have a really simple way to do it, I dont think simply making a new key file is a useful option.

Thanks!!

[Ram]

FASTA header editing is a widely discussed topic on the forum. Have you searched the forum for existing posts?

[clmattson]

Yes, but for some reason none of the suggested answers in the posts I found already worked, or they were exclueively for cases with exact matching. which was suprising to me bc I usually find awesome solutions on BioStars within 10 mins or so.... I figured out a sort of janky work around but after like an hour of trying to get old solutions to work I was ready to give up. will post said janky work around in a bit lol

Answer 1

[shenwei356]

I've tried seqkit replace, but it doesnt seem to work unless the keys match the existing headers exactly,

$ seqkit replace -p '^(.+?)/(.+)$' -r '{kv}_$2' -k sample_key.txt samples.fasta 
[INFO] read key-value file: sample_key.txt
[INFO] 4 pairs of key-value loaded
>AAA_contig002
ATCG
>def456_contig001
GCTA
>H-10_contig003
CAGT

Answer 2

[Mensur Dlakic]

Someone here probably knows how to do this in a single line or two, but this may still be helpful. I suggest you make a copy of samples.fasta before running any of these commands. Everything must be pasted exactly as below, because single- and double-quotations are not interchangeable.

Replacing the slash with an underscore is simple:

perl -pi -e 's/\//_/g' samples.fasta

Create a script that will take first-column values from sample_key.txt and replace them with second-column values:

awk '{print "perl -pi -e ^s/"$1"/"$2"/g^ samples.fasta"}' sample_key.txt > script.sh
perl -pi -e "s/\^/\'/g" script.sh

Run the script and delete it when done:

source script.sh
rm script.sh