anvi-script-gen_stats_for_single_copy_genes.py

A simple script to generate info from search tables, given a contigs-db.

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Authors

Can consume

contigs-db

Can provide

genes-stats

Usage

This program provides information about each of the single-copy core genes in your contigs-db.

Simply provide a contigs-db, and it will create a genes-stats file containing a variety of information about the single copy core genes in your database.

This is kind of an old anvi’o script that we still keep around because history. But if you are here, you may also consider taking a look at the programs anvi-script-gen-hmm-hits-matrix-across-genomes and anvi-get-sequences-for-hmm-hits.

The console output will tell you the total number of contigs, splits, and nucleotides in your contigs-db, while the text output will tell you the source, name, and e-value of each single-copy core gene.

You can get information from only single-copy core genes from a specific source. To see what sources are available in your contigs-db, run

Edit this file to update this information.

Additional Resources

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.