haradama / plasmidpicker

Software to identify plasmid sequence data from metagenome using logistic regression and Minhash

Requirements

• numpy
• cython
• biopython
• click
• mmh3
• h5py

Installation

git clone https://github.com/haradama/PlasmidPicker.git
cd PlasmidPicker
pip install -r requirements.txt
python setup.py install

Usage

Usage: plasmidpicker pick [OPTIONS]

  Detect plasmid sequence data in metagenome.

Options:
  -i, --infile TEXT        Specify FASTA input file
  -t, --threshold INTEGER  Threshold of probability (0 <= t <= 100) [70]
  -l, --length INTEGER     Threshold of contig's length [1000]
  -d, --outdir TEXT        Output directory [.]
  --help                   Show this message and exit.

Usage: plasmidpicker classify [OPTIONS]

  Perform similarity search of plasmids using MinHash.

Options:
  -i, --infile TEXT     Specify FASTA input file
  -s, --sketch INTEGER  Sketch size (1 <= s <=1000) [1000]
  -l, --length INTEGER  Threshold of contig's length [1000]
  -hi, --hits INTEGER   Number of hits to display [5]
  -o, --outfile TEXT    Output file [result.txt]
  --help                Show this message and exit.

License