anvi-export-structures

Authors
Requires
Can use
Provides
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

Export .pdb structure files from a structure database.

🔙 To the main page of anvi’o programs and artifacts.

Authors

Evan Kiefl

Requires

structure-db

Can use

genes-of-interest-txt

Provides

protein-structure-txt

Usage

This program exports the structures from a structure-db into the globally understood pdb format (protein-structure-txt), so they may be used for any follow-up analyses taking place outside of anvi’o.

To run, just provide a structure-db and an output path:

anvi-export-structures -s structure-db \ -o path/to/output

You can also provide a list of gene caller IDs, either directly through the parameter --gene-caller-ids or through a file with one gene caller ID per line.

Edit this file to update this information.

Command line interface

The following is the list of parameters and their descriptions in the latest version of anvi-export-structures.

The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).

Command line usage

anvi-export-structures [-h] -s STRUCTURE_DB [-o DIR_PATH] [--gene-caller-ids GENE_CALLER_IDS] [--genes-of-interest FILE]

Parameters and their descriptions

options

-s, --structure-db STRUCTURE_DB required: Anvi'o structure database.
-o, --output-dir DIR_PATH: Directory path for output files
--gene-caller-ids GENE_CALLER_IDS: Gene caller ids to focus on. Multiple of them can be declared separated by a delimiter (the default is a comma, and if there is no option to change the delimiter, you must use a comma).In anvi-gen-variability-profile, if you declare nothing you will get all genes matching your other filtering criteria. In other programs, you may get everything, nothing, or an error. It really depends on the situation. Fortunately, mistakes are cheap, so it's worth a try.
--genes-of-interest FILE: A file with anvi'o gene caller IDs. There should be only one column in the file, and each line should correspond to a unique gene caller id (without a column header).

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.