FredHutch/integrate-metagenomic-assemblies

Name: integrate-metagenomic-assemblies

Owner: Fred Hutchinson Cancer Research Center

Description: Combine a set of metagenomic assemblies into a common set of references

Created: 2018-04-10 22:18:04.0

Updated: 2018-05-10 23:00:23.0

Pushed: 2018-05-10 23:10:11.0

Homepage: null

Size: 2978

Language: Python

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README

Integrate Metagenomic Assemblies

Combine a set of metagenomic assemblies into a common set of references

Inputs

To use this software, generate a set of assemblies with predicted protein-coding genes in a single FASTA file (e.g. *.fastp.gz) and the annotations in GFF format.

All of those files should be found in a single folder, with the name of the file matching the name of the sample that the assembly originated from.

Outputs

After running this code, two files should be generated:

1. A FASTA file with the deduplicated protein-coding gene sequences
2. A JSON file describing the identity and physical relationship between those protein-coding sequences

The format of the JSON will be as follows:

{
    "protein_id": "<name of deduplicated reference>",
    "members": [
        "<ids of assembled proteins within the group>"
    ],
    "annotation": "<annotation of protein>",
    "neighbors": {
        "<upstream or downstream>": {
            "<protein id of upstream neighbor>": "<number of assemblies with connection>"
        }
    }
},
{
    "etc"
}

Invocation

grate_assemblies.py \
--gff-folder "<folder containing GFF files>" \
--prot-folder "<folder containing protein FASTA files>" \
--output-name "<base name for output files>" \
--output-folder "<folder for output files>"

integrate_assemblies.py -h for more options.

Installation

To use this code, we recommend using the Docker image, because it contains all the needed dependencies and is validated with a set of tests. If that is not a satisfying option, see the Dockerfile to see how to set up the appropriate environment.