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 -
1 answer
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!
- install
fasta file validator from pip or conda.
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If you need empty records to be considered invalid, maybe you could issue a pull request to biopython
Must check this using seqkit
https://bioinf.shenwei.me/seqkit/usage/#seq
You could subclass the SeqIO operations and extend the sequence checking processes for empty seqs etc?