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sbx_gene_clusters

Tests Super-Linter

Reads-level based alignment to gene clusters of interest, e.g. bai operon or butyrate producing genes. Please refer to sunbeam_database for details. Make a diamond database from your proteins of interest fasta file and provide a text annotation file with the following columns: geneID, proteinID, ARO, taxon, weight.

Installation

To install, activate your conda environment (using the name of your environment) and use sunbeam extend:

conda activate <i>sunbeamX.X.X</i>
sunbeam extend https://github.com/sunbeam-labs/sbx_gene_clusters.git

Now take UniRef50 database as an example. First download the uniref50.fasta into your current sunbeam_output/mapping/sbx_gene_family/databases/.

mkdir -p sunbeam_output/mapping/sbx_gene_family/database/
wget ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.fasta.gz -P sunbeam_output/mapping/sbx_gene_family/database/

Be sure to update the config.yml with the proper path.

Usage

To generate alignments,

sunbeam run --profile /path/to/project all_gene_clusters

Configuration

  • threads: Is the number of threads to run parallel processes with
  • genes_fp: Is the path to the downloaded database
  • evalue:
  • alnLen:
  • mismatch:

Legacy Installation

For sunbeam versions <3 or if sunbeam extend isn't working, you can use git directly to install an extension:

git clone https://github.com/sunbeam-labs/sbx_gene_clusters.git extensions/sbx_gene_clusters

and then include it in the config for any given project with:

cat extensions/sbx_gene_clusters/config.yml >> /path/to/project/sunbeam_config.yml