Javascript Error: too much recursion

[raw937]

python 3.11
latest version of codonU

Any thing I try within the examples for my file I get "Javascript Error: too much recursion"

any thoughts?

[raw937]

I figured it out. It does like .ffn, .fna, or .fnn.fasta only .fasta. Odd?

[SouradiptoC]

I am not sure what in this case you were trying to do and how you are having a js error. CodonU completely runs in python. If you are using jupyter, then you may face such an error. Let me know how you face the error and what you were trying to do.

P.S. CodonU only take as input .fasta file. No other extensions are supported.

[raw937]

This is from a notebook with .ffn, .fna, .faa extensions which are commonly used formats.

[SouradiptoC]

As of now, handler for opening only .fasta is available. It would be better if you can change the extensions to .fasta. Thanks for bringing in notice the other commonly used formats. I'm working on an update, i'll try to incorporate handlers for those extensions also.

[raw937]

It is quite confusing to use .fasta for all outputs.

The .fasta isn't commonly used due to this confusion.

.fna = fasta nucleotide files for contigs or reads
.faa = fasta amino acid for called ORFs
.ffn = fasta nucleotide feature format which the nucleotide version of .faa

You need a .ffn for this program to run correctly. If you just add a whole genome or a collection of contigs this program will fail to run.

This would be useful to have this content in the readme to help users.

[SouradiptoC]

Thanks for the suggestions. As mentioned earlier, I'll look into handlers for other file formats.

[SouradiptoC]

Hey @raw937, I looked into .fna, .faa, .ffn formats. As per my understanding, the difference between these formats and .fasta are merely semantical and not structural. The contents of these file as well look like the following

> [id] [name] [desc]
code (80 chars)

I got your point that having specified extensions will help users to know the contents of the file, but after all, parsing the contents of the file are same as that of .fasta. So, I'm not getting why you faced the error in the first place. Can you please share the exact process you were following and some dummy data so that I can reproduce the error?

[Hasanzahid10]

Hello sir,
I am new user CodonU .I have one question about output.
I am run Staphylococcus_aureus.fasta file but my output not to same your output.
why.. if you want I will share my output screenshot ............