- numpy
- cython
- biopython
- click
- mmh3
- h5py
git clone https://github.com/haradama/PlasmidPicker.git
cd PlasmidPicker
pip install -r requirements.txt
python setup.py install
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.