Updating Plasmidfinder Blast Database "enterobacteriaceae" to "enterobacteriales"

[emarinier]

Fixes #169 and #177.

There's nothing automatic here though. I don't know if you wanted it automatically build the list from the downloaded database files. Let me know!

[apetkau]

Thanks so much Eric, this looks great.

Change request

In addition to the in-line comment, can you also update the CHANGELOG.md to what has been changed?

Description of automation

For automating the list of available database (fasta) files for PlasmidFinder, this is already implemented.

On the PlasmidFinder website (https://cge.food.dtu.dk/services/PlasmidFinder/), there are two options to select:

However, in the underlying fasta files, there are more than two options (https://bitbucket.org/genomicepidemiology/plasmidfinder_db/src/master/). However, these map on to two different labels Enterobacteriales and Gram Positive as defined in the config file.

This mapping is already handled by StarAMR by reading the config file in the underlying installed PlasmidFinder database:

staramr/staramr/blast/plasmidfinder/PlasmidfinderBlastDatabase.py

Lines 33 to 35 in 1982053

	if database_type == 'gram_positive' and 'gram_positive' not in existing_database_types:
	config_df = self.get_config_table(database_dir)
	self.database_names = config_df.loc[config_df["name"] == "Gram Positive", "db_prefix"].tolist()

Hence, there is no need to update this list.

[emarinier]

Okay, I think it should be good now.

[apetkau]

Looks good to me. Thanks so much.