resAnnotator.py

Description: searches amino acid sequence against known ARG specific databases sequentially and assigns annotation using BLAST and HMM approach.

Usage

  resAnnotator [-h] -i INPUT_SEQUENCE -o OUTPUT_DIR -c CONFIG_FILE
                [--clean] [-t NUM_THREADS] [-p PREFIX] [-v]

  ResAnnotator - 0.5.0 - The program assigns antibiotic resistance function
  using blast and HMM based databases

  optional arguments:
  -h, --help            show this help message and exit
  -i INPUT_SEQUENCE, --input_sequence INPUT_SEQUENCE
                    input file must be in FASTA format (contig and
                    protein)
  -o OUTPUT_DIR, --output_dir OUTPUT_DIR
                    specify output folder
  -c CONFIG_FILE, --config CONFIG_FILE
                    path to the config file
  --clean               removes temporary files
  -t NUM_THREADS, --num_threads NUM_THREADS
                    number of threads to use(default=4)
  -p PREFIX, --prefix PREFIX
                    prefix for the output files
  -v, --version         prints software version number

A program to annotate antibiotic resistance genes/proteins in contigs/protein
sequences using BLAST(Uniprot, CARD, Resfinder) and/orHMM (Resfams, PFam-A)
databases

Config file template: example_config_file.txt