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Proteins

pharokka v1.4.0 implements pharokka_proteins.py, allows for the fast annotation of Amino Acid FASTA formatted input proteins with PHROGs, CARD and VFDB.

You can run pharokka_proteins.py in the following way (most basic command below). By default this will run MMSeqs2 on PHROGs, CARD and VFDB, along with PyHMMER on PHROGs

pharokka_proteins.py -i <inpu protein FASTA file> -d <database directory> -o <output folder> -t <threads>

To run only PHROGs with HMMs (PyHMMER), use --hmm_only

pharokka_proteins.py -i <input protein FASTA file> -d <database directory> -o <output folder> -t <threads> --hmm_only

To run only MMseqs2 on PHROGs, CARD and VFDB, use --mmseqs2_only

pharokka_proteins.py -i <input protein FASTA file> -d <database directory> -o <output folder> -t <threads> --mmseqs2_only

Output

pharokka_proteins.py generates 3 output files:

  • _proteins.faa containing the original protein FASTA file with the header updated with the new PHROG annotation
  • _proteins_full_merged_output.tsv containing the full information for each protein, similar to _cds_functions.tsv for pharokka.py but without the gene prediction information. This will include VFDB and CARD information.
  • _proteins_summary_output.tsv containing the following 5 columns (where ID is name of each inputprotein)

ID length (AA) phrog annot category

e.g.

ID length phrog annot category
protein_1 456 3717 terminase large subunit head and packaging
protein_2 243 315 endolysin lysis 
usage: pharokka_proteins.py [-h] [-i INFILE] [-o OUTDIR] [-d DATABASE] [-t THREADS] [-f] [-p PREFIX] [-e EVALUE] [--hmm_only] [--mmseqs2_only] [-V] [--citation]

pharokka_proteins.py: fast phage protein annotation script

options:
  -h, --help            show this help message and exit
  -i INFILE, --infile INFILE
                        Input proteins file in amino acid fasta format.
  -o OUTDIR, --outdir OUTDIR
                        Directory to write the output to.
  -d DATABASE, --database DATABASE
                        Database directory. If the databases have been installed in the default directory, this is not required. Otherwise specify the path.
  -t THREADS, --threads THREADS
                        Number of threads. Defaults to 1.
  -f, --force           Overwrites the output directory.
  -p PREFIX, --prefix PREFIX
                        Prefix for output files. This is not required.
  -e EVALUE, --evalue EVALUE
                        E-value threshold for MMseqs2 database PHROGs, VFDB and CARD and pyhmmer PHROGs database search. Defaults to 1E-05.
  --hmm_only            Runs pyhmmer (HMMs) with PHROGs only, not MMseqs2 with PHROGs, CARD or VFDB.
  --mmseqs2_only        Runs MMseqs2 with PHROGs, CARD and VFDB only (same as Pharokka v1.3.2 and prior).
  -V, --version         Print pharokka Version
  --citation            Print pharokka Citation