Default Partitions from Custom Flat files List

Default Partitions from a Custom list of flat files

If you prefer to use existing local Genbank flatfiles instead of downloading new files you can provide a file list to the database command.

Step 1:

Acquire a set of Genbank Flatfiles to be processed.

Step 2:

Mirror the GenBank Taxonomy FTP. Only the accession2taxid/ folder and taxdump.tar.gz are required.

Step 3:

The following command will build a FASTA datastore from a file list of GenBank flat files. The filename passed to the --ff_list will be used to identify the datastore and can be used with the --customdb argument in the custom_db command. The arguments --build_only, --path, --taxonomy_path, and --ff_list are required to create the database from a file list.

mtsv_setup database --path today --thread 4 --build_only --taxonomy_path pub/taxonomy/ --ff_list file_list.txt

Example of Flatfile file list:

• file_list.txt. The file should contain absolute paths to the desired GenBank Flat files (The flat files maybe zipped or unzipped).

Step 4:

Create FM-indexes consisting of default taxonomic partitions described here using the "files" custom database.

mtsv_setup custom_db --path today --thread 4 --customdb file_list                   

More Examples:

The following command would build 3 fm-indices using B. cereus, B. anthracis and a combination of them. Using the complete genome assemblies with 2 cores. No .txt extension for --customdb files

mtsv_setup custom_db --path today --thread 2 --partition 1396 1392 1396,1392 --customdb file_list