-
Notifications
You must be signed in to change notification settings - Fork 82
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Antismash v5.0 isn't being parsed #292
Comments
Yippeee! Always fun when formats change..... is there a tag saying which version of antismash the result is from? Edit: looks like version in the comment section. So an updated parser will need to be added to the code. |
yea, in the .gbk they have this: ##antiSMASH-Data-START## but there isn't a tag such as this in the v4 .gbk's |
In the example you posted above, it seems that the annotation is not numerically incrementing properly, ie there are two 'protocluster' features, however, they say there are from the same "number". Is this the case throughout the gbk file output?
And then is one other one, looks like this:
So I'm wondering if this is correct? These two "protocluster" features are part of the same cluster? Or is this a mistake? Does the html output match this? They appear to overlap -- so perhaps underlying code is correct. So does that mean that all "clusters" have this protocluster annotation or is this a subset of the cluster annotation? |
I didn't use the same genome ;) |
Goal is to get this updated today, I'll post here when its working. |
Okay, I think I have it fixed, if you wouldn't mind testing the latest commit that would be helpful. Version should be:
|
The parser picked up on clusters and smCOGs, but stated that I don't have any backbone biosynthetic enzymes. While I believe I do have some as antiSMASH is picking up some genes are "core biosynthetic genes".
|
Ok, thanks. Its not really a big deal/change, I don't think, as it is simply a counter. Do the results in Wonder if this is difference in 5.0.0 [what I ran on web server] and 5.0.0rc1 [which seems to be what you have]. |
Yes, the results in |
Thanks, I'll see if I can fix the counter. |
Okay, should now be counting the biosynthetic enzymes based on the 'gene_kind' = 'biosynthetic' in the CDS metadata. |
Thank you |
So this fixed worked on all my genomes except one, where I got this error:
|
Thanks, that one was typo: 0c6732d. git pull should fix it. |
Got it to work |
I am currently using the latest version which I pulled off of github today (v1.5.3-21ad095).
I am also using the newest version of antiSMASH v5, however, I noticed that the qualifiers in the .gbk output are different than previous .gbk that I had from antiSMASH v4. Perhaps these could be why not clusters or smCOGs are being parsed out.
I have attached my log file and a version of the .gbk results showing a portion of the output of antiSMASH v5.
funannotate-annotate.log
antiSMASH.results.txt
The text was updated successfully, but these errors were encountered: