DNA sequence hashing

[avilella]

Feature request:

Given a DNA sequence, convert into a number by hashing in base 2 as shown below:

mapping = {'A': '00', 'T' = '01', 'G': '10', 'C' = '11'}

produce a value of zero if there are non-ACGT values.
For RNA, we could have T=U in case there are Us.

Example:

cat file.fasta | seqkit hash -t DNA
>foo
348128344908321234
>bar
32049201394320

Maybe the output should be tabular as the output of seqkit fx2tab?

Maybe this is already somehow implemented internally in the deduplication code, not sure. It's useful (for me) when wanting to give a short(ish) numerical value that would be unique to each unique DNA sequence. Thx

[shenwei356]

Yes, it's easy to implement. Just call a fast hash function on any sequence (string), but it's irreversible.
Similarly, unikmer encode can convert dna/rna (<=32bp）to reversible uint64 values.

[shenwei356]

Implemented in seqkit fx2tab -s/--seq-hash, and it's case sensitive.

For DNA/RNA transform, use seqkit seq --dna2rna/--rna2dna, and seqkit seq -l/--lower-case/-u/--upper-case for letter case.

[jolespin]

I use this to get [id][hash]

pv query.fasta.gz | seqkit fx2tab -s -n > id_to_hash.tsv