Any packages to validate FASTA file?

Question

[khaeuk]

I am trying to create a function that can take in a file and check to see if it's a valid fasta file or not (such as making sure there's no leading tabs or spaces, the first character starts with >, no empty lines between sequences, etc.).

I have tried using SeqIO.parse(filename, "fasta"), but it returned true for cases where it only had the description line with > and no sequence provided.

I was trying to code this, but I was wondering if there was other packages that checks validity of FASTA format?

Thanks -

[lakhujanivijay]

Must check this using seqkit

https://bioinf.shenwei.me/seqkit/usage/#seq

[mrals89]

If you need empty records to be considered invalid, maybe you could issue a pull request to biopython

[Joe]

You could subclass the SeqIO operations and extend the sequence checking processes for empty seqs etc?

Answer 1

[Ankit]

There are two options: you can use accordingly: 1 : https://github.com/linsalrob/fasta_validator fasta_validator This is simple C code to validate a fasta file. It only checks a few things, and by default only sets its response via the return code, so you will need to check that!

1. install fasta file validator from pip or conda.