Depencencies:
- bedtools
- CD-HIT
- BLAST
- DIAMOND
- MCL
- pandas
- SeqIO
The simplest method is installed via conda:
-
Download and install the appropriate conda, such as miniconda from here
-
Create a conda environment with all the necessary dependencies: From the repository directory run
conda create -y -c conda-forge -c defaults --name panta python=3.10 mamba
conda activate panta
mamba install -y -c conda-forge -c bioconda -c anaconda -c defaults --file requirements.txt
pip install .
Or via docker:
docker pull amromics/panta:latestif you want to build the image yourself:
docker build -t amromics/panta:latest .Activate conda enviroment:
source activate panta
usage: panta main [-h] [-g [GFF ...]] [-f TSV] -o OUTDIR [-s] [-b {diamond,blast}] [-i IDENTITY] [--LD LD] [--AL AL] [--AS AS] [-e EVALUE]
[-t THREADS] [--table TABLE] [-a [{nucleotide,protein} ...]]
Main pipeline: run pan-genome analysis for the first time
options:
-h, --help show this help message and exit
-g [GFF ...], --gff [GFF ...]
gff input files (default: None)
-f TSV, --tsv TSV tsv input file (default: None)
-o OUTDIR, --outdir OUTDIR
output directory (default: None)
-s, --dont-split dont split paralog clusters (default: False)
-b {diamond,blast}, --blast {diamond,blast}
method for all-against-all alignment (default: diamond)
-i IDENTITY, --identity IDENTITY
minimum percentage identity (default: 0.7)
--LD LD length difference cutoff between two sequences (default: 0.7)
--AL AL alignment coverage for the longer sequence (default: 0)
--AS AS alignment coverage for the shorter sequence (default: 0)
-e EVALUE, --evalue EVALUE
Blast evalue (default: 1e-06)
-t THREADS, --threads THREADS
number of threads to use, 0 for all (default: 0)
--table TABLE codon table (default: 11)
-a [{nucleotide,protein} ...], --alignment [{nucleotide,protein} ...]
run alignment for each gene cluster (default: None)
usage: panta add [-h] [-g [GFF ...]] [-f TSV] -c COLLECTION_DIR [-s] [-b {diamond,blast}] [-i IDENTITY] [--LD LD] [--AL AL] [--AS AS]
[-e EVALUE] [-t THREADS] [--table TABLE] [-a [{nucleotide,protein} ...]]
Add pipeline: add sample into previous collection
options:
-h, --help show this help message and exit
-g [GFF ...], --gff [GFF ...]
gff input files (default: None)
-f TSV, --tsv TSV tsv input file (default: None)
-c COLLECTION_DIR, --collection-dir COLLECTION_DIR
previous collection directory (default: None)
-s, --dont-split dont split paralog clusters (default: False)
-b {diamond,blast}, --blast {diamond,blast}
method for all-against-all alignment (default: diamond)
-i IDENTITY, --identity IDENTITY
minimum percentage identity (default: 0.7)
--LD LD length difference cutoff between two sequences (default: 0.7)
--AL AL alignment coverage for the longer sequence (default: 0)
--AS AS alignment coverage for the shorter sequence (default: 0)
-e EVALUE, --evalue EVALUE
Blast evalue (default: 1e-06)
-t THREADS, --threads THREADS
number of threads to use, 0 for all (default: 0)
--table TABLE codon table (default: 11)
-a [{nucleotide,protein} ...], --alignment [{nucleotide,protein} ...]
run alignment for each gene cluster (default: None)
Basic:
panta main -o examples/test/output -g examples/test/main/*.gff
panta add -c examples/test/output -g examples/test/add/*.gff
Via docker from the repository directory run:
docker run -it --rm -v $PWD:/tmp amromics/panta:latest panta main -o examples/test/output -g examples/test/main/*.gff