Microbial 'omics

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anvi-script-gen-genomes-file [program]

Generate an external genomes or internal genomes file.

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Iva Veseli

Usage

The primary purpose of this script is to reduce the amount of labor required to generate external-genomes or internal-genomes files anvi’o typically uses to learn about your bins and/or genomes.

Generating an external genomes file

If you provide an input directory and a name for the output file, then every contigs-db in that directory will get a line in the resulting external-genomes file:

anvi-script-gen-genomes-file --input-dir path/to/dir \
--output-file external_genomes.txt


Names for genomes in the the resulting external genomes file will be set based on the project_name variable, and the contigs_db_path column will contain absolute paths.

You can learn the current project_name and/or change it for a given contigs-db using the program anvi-db-info. This variable is set by the program anvi-gen-contigs-database.

You can also instruct anvi-script-gen-genomes-file to include all subdirectories under a given directory path:

anvi-script-gen-genomes-file --input-dir path/to/dir \
--output-file external_genomes.txt \
--include-subdirs


Generating an internal genomes file

To get an internal-genomes file containing all bins from a collection, provide a profile-db, its corresponding contigs-db, and the collection name:

anvi-script-gen-genomes-file -c contigs-db \ -p profile-db \ -C collection \ --output-file internal-genomes.txt

The name of each internal genome will be the same as the bin name, and the path columns will contain absolute paths.

Edit this file to update this information.

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.