anvi-export-contigs

Authors
Requires
Can use
Provides
Usage

Splits mode

Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

Export contigs (or splits) from an anvi'o contigs database.

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

Authors

A. Murat Eren (Meren)

Requires

contigs-db

Can use

genes-of-interest-txt

Provides

contigs-fasta

Usage

This program exports the contig sequences from a contigs-db, outputting them as a contigs-fasta. It also has the ability to output the sequences of your splits instead.

You can run this program as follows, which will return ALL contigs in a given contigs-db file:

anvi-export-contigs -c contigs-db \ -o path/to/contigs-fasta

You can also limit the contigs you may be interested in to a subset by providing the list of contig names you wish to export in a file. For example:

anvi-export-contigs -c contigs-db \ -o path/to/contigs-fasta \ --contigs-of-interest my_favorite_contigs.txt

where my_favorite_contigs.txt looks like this:

contig_0001
contig_0005
contig_0035

Alternatively, you may be interested in contigs that include one or more genes you are interested. In that case you can use --genes-of-interest with a genes-of-interest-txt, and anvi’o will export only those contigs that contain at least one of the gene calls you listed:

anvi-export-contigs -c contigs-db \ -o path/to/contigs-fasta \ --genes-of-interest my_favorite_genes.txt

where my_favorite_genes.txt looks like this:

5
13
206

Please note that --contigs-of-interest and --genes-of-interest are mutually exclusive: you can use one or the other in a given command, but not both at the same time.

Splits mode

Want to look at your splits instead of your contigs? Just run with the flag splits-mode attached.

anvi-export-contigs -c contigs-db \ -o path/to/contigs-fasta \ --splits-mode

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-contigs.

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-contigs [-h] -c CONTIGS_DB [--contigs-of-interest FILE] [--genes-of-interest FILE] [--splits-mode] -o FILE_PATH [--just-do-it] [--no-wrap]

Parameters and their descriptions

options

-c, --contigs-db CONTIGS_DB required: Anvi'o contigs database generated by 'anvi-gen-contigs-database'
--contigs-of-interest FILE: It is possible to focus on only a set of contigs. If you would like to do that and ignore the rest of the contigs in your contigs database, use this parameter with a flat file every line of which desribes a single contig name.
--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).
--splits-mode: Export split sequences instead.
-o, --output-file FILE_PATH required: File path to store results.
--just-do-it: Don't bother me with questions or warnings, just do it.
--no-wrap: Do not be wrap sequences nicely in the output file.

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.