BiGFAM taxonomy extraction

[OmkarSaMo]

Is there a way to extract more information from the BiGFAM GCFs in tabular format?

For example can we get a table with information on distribution of BGCs across genera, a table of all core members of the GCF, and possibly also the genbank files of each BGC in the GCF core members for downstream analysis (https://bigfam.bioinformatics.nl/run/6/gcf/214329)

[matinnuhamunada]

Yes, everything is the sqlite.db file, perhaps it is easier to define the final table then built the sql query script:

[matinnuhamunada]

In the meanwhile, this can be done from metabase:

• run metabase with:

bgcflow --snakefile workflow/Metabase

Load the SQLite database, for example:

• BiG-FAM Query: data/interim/bigslice/query/mq_saccharopolyspora_antismash_6.1.1/5.db
• BiG-FAM db: resources/bigslice/full_run_result/result/data.db