Comments (6)
Do you have any advice on how to best scrape the json file for information on identified clusters, similarity, regions and such.
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We no longer generate the geneclusters.txt file because the format did not accommodate the updated region concept in a meaningful way.
All the data is in the JSON output file in a machine-readable format, you can extract in information relevant to your research question from that. There's tons of resources on how to work with JSON data on the internet.
from antismash.
Okay thanks, to be sure, the JSON you would refer to is >sample_name<.json?
from antismash.
yes
from antismash.
This also has the whole sequence at the top of the json file right?
from antismash.
Yes, the whole point of that file is to allow antiSMASH to re-use previous results when re-running with different parameters. It has all the data.
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Related Issues (20)
- Malformed record in ClusterBlast database HOT 1
- too many problem of python package "biopython" HOT 6
- error during antismash7 install - "ERROR: Could not build wheels for ..." HOT 11
- Some terpene synthases missed.
- Error:pip install antismash-7.1.0 HOT 6
- blastp -> ['Error: The sequences are expected to be proteins but only contain DNA letters. HOT 1
- Completely include (or exclude) features sitting on the edge of a candidate cluster HOT 13
- Local antiSMASH and web server showed different Cluster blast results. HOT 6
- Some protoclusters in a "neighbouring candidate cluster" don't belong to anyone of the other kinds of candidate clusters HOT 2
- Can I only run comparison algorithm?
- Job Submission Failed HOT 1
- https://dl.secondarymetabolites.org/ seems to be down, unable to curl docker image HOT 1
- Genbank SMILES qualifier has extra space for long products HOT 2
- Question about fungal mode HOT 1
- Record xxx contains no genes bug when parsing gbk file HOT 1
- docker run problem HOT 1
- Antismash RuntimeError HOT 1
- Error: could not parse records from GFF3 file HOT 8
- Feature Request: Discard empty and rRNA/tRNA unique contigs HOT 5
- scikit-learn 0.19.0 requirement causes 'legacy-install-failure' HOT 2
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from antismash.