anvi-gen-hmm-hits-matrix

Authors
Requires
Can use
Provides
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

A simple script to generate a TAB-delimited file that reports the frequency of HMM hits for a given HMM source across contigs databases.

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Authors

A. Murat Eren (Meren)

Requires

external-genomes

Can use

internal-genomes hmm-source hmm-hits

Provides

hmm-hits-across-genomes-txt

Usage

This program lets you look at the hmm-hits from a single hmm-source across multiple genomes or bins, by creating a hmm-hits-across-genomes-txt.

For a simlar program that reports function hits across genomes, see anvi-gen-function-matrix.

The input of this program can be either an internal-genomes or an external-genomes.

Here are two example run on an internal-genomes:

anvi-gen-hmm-hits-matrix -i internal-genomes \ --hmm-source Bacteria_71 \ -o output.txt

To list the hmm-sources common to the datasets that you’re analyzing, just add the flag --list-hmm-sources, as so:

anvi-gen-hmm-hits-matrix -e external-genomes \ --list-hmm-sources

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-gen-hmm-hits-matrix.

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-gen-hmm-hits-matrix [-h] [-e FILE_PATH] [-i FILE_PATH] [--hmm-source HMM_ANNOTATION_SOURCE] [-l] -o FILE_PATH [--skip-checking-genome-hashes]

Parameters and their descriptions

INPUT: INTERNAL/EXTERNAL GENOMES FILE Yes. You need to use an internal and/or external genomes file to tell anvi'o where your contigs databases are.

-e, --external-genomes FILE_PATH: A two-column TAB-delimited flat text file that lists anvi'o contigs databases. The first item in the header line should read 'name', and the second should read 'contigs_db_path'. Each line in the file should describe a single entry, where the first column is the name of the genome (or MAG), and the second column is the anvi'o contigs database generated for this genome.
-i, --internal-genomes FILE_PATH: A five-column TAB-delimited flat text file. The header line must contain these columns: 'name', 'bin_id', 'collection_id', 'profile_db_path', 'contigs_db_path'. Each line should list a single entry, where 'name' can be any name to describe the anvi'o bin identified as 'bin_id' that is stored in a collection.

HMM STUFF This is where you can specify an HMM source, and/or a list of genes to filter your results.

--hmm-source HMM_ANNOTATION_SOURCE: Use a specific HMM source. You can use '--list-hmm-sources' flag to see a list of available resources. The default is 'None'.
-l, --list-hmm-sources: List available HMM sources in the contigs database and quit.

OUTPUTTAH

-o, --output-file FILE_PATH required: File path to store results.
--skip-checking-genome-hashes: Use this flag if you would like anvi'o to skip checking genome hashes. This is only relevant if you may have genomes in your internal or external genomes files that have identical sequences with different names AND if you are OK with it. You may be OK with it, for instance, if you are using `anvi-dereplicate-genomes` program to dereplicate genomes desribed in multiple collections in an anvi'o profile database that may be describing the same genome multiple times (see https://github.com/merenlab/anvio/issues/1397 for a case).

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.