anvi-script-pfam-accessions-to-hmms-directory

You give this program one or more PFAM accession ids, and it generates an anvi'o compatible HMM directory to be used with anvi-run-hmms.

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Authors

A. Murat Eren (Meren)
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Georges Kanaan (Gio)
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Requires

pfam-accession pfams-data

Provides

hmm-source

Usage

You give this program one or more PFAM accession ids, and it generates an anvi’o compatible HMM directory hmm-source to be used with anvi-run-hmms by downloading them from the PFAM database.

Basic usage

You may either specify a list of PFAM accessions with --pfam-accessions-list:

anvi-script-pfam-accessions-to-hmms-directory --pfam-accessions-list PF00001 PF00002 \ -o PROFILE-NAME

Or a file containing this list using --pfam-accessions-file. The file should have one accession number per line:

anvi-script-pfam-accessions-to-hmms-directory --pfam-accessions-file file.txt \ -o PROFILE-NAME

Please note that the PROFILE-NAME will become the name for the HMM source when you use this HMM directory with anvi-run-hmms. So choose the output directory name accordingly, and make sure (1) it does not conflict with any existing HMM source name in your anvi’o setup, and (2) it is descriptive of the profile you are building.

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-script-pfam-accessions-to-hmms-directory.

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-script-pfam-accessions-to-hmms-directory [-h] [--pfam-accessions-list PFAM_ACCESSION [PFAM_ACCESSION ...]] [--pfam-accessions-file FILE] [-o DIR_PATH]

Parameters and their descriptions

options
--pfam-accessions-list PFAM_ACCESSION
One or more PFAM accession IDs (such as PF14437). If you have multiple accessions, you can separate them from each other with a space. If you have too many, consider using the `--pfam-accessions-file` parameter instead.
--pfam-accessions-file FILE
A single column text file where each column is a single PFAM accession ID (such as PF14437). You may have as many accession ids as you like in this file.
-o, --output-dir DIR_PATH
Output directory for the anvi'o-formatted HMMs. Choose the name wisely as this will be the name that will appear in the contigs database after you provide it with the `-H` flag to `anvi-run-hmms`. We suggest you use a name that does not include any of those millenial characters (like space, question mark, comma, and such, you know).

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.

Copyleft, The anvi'o Project