how to sort fasta file according to a header file

Question

[Nelo]

Hi!

I have two files: one is protein fasta file (a.fa) & another is header.txt. I want to get my sequences in the same order as the header file. How can I do this?

[Mensur Dlakic]

This is a type of a question where the only appropriate response is "Would you like fries with your order?"

You are not showing any previous effort to solve this problem. There is also a search function which you don't seem to have tried.

This is not a service website where you simply come and make an order, and assume that someone will jump right at it and do your work for free.

[GenoMax]

I wanted to get my sequences in the same order as

That is not a simple sort then? Are you selecting specific sequences or just want to sort based on an external file?

[Nelo]

awk 'NR==FNR{a[$0]; next} /^>/{if($1 in a) print $0; flag = $1 in a ? 1 : 0; next} flag' header.txt a.fa >reordered.fasta

this is the one I tried, but it is not giving the dersired output I want

[Ram]

Your response does not answer GenoMax's question. "Are you selecting specific sequences or just want to sort based on an external file?"

Answer 1

[shenwei356]

Just use seqkit faidx a.fa -l headers.txt, usage.

$ cat s.fa
>1
a
>2
c
>3
t

$ cat headers.txt 
2
3
1

$ seqkit faidx s.fa -l headers.txt 
[INFO] 3 patterns loaded from file
[INFO] create or read FASTA index ...
[INFO] create FASTA index for s.fa
>2
c
>3
t
>1
a

Answer 2

[tshtatland]

Use seqkit fx2tab and seqkit fx2tab to convert between fasta and tsv. See:

• format conversion - How to convert fasta file to tab delimited file - Bioinformatics Stack Exchange
• bioinformatics - Sort FASTA file according to length of sequences - Stack Overflow

Use awk or Perl to sort the resulting tsv file based on another file. See:

• linux - sort a file based on a column in another file - Stack Overflow