tbrekalo / mini

minimizer extraction with python bindings

mini

Minimizer extraction in python with c++ implementation

Requirements

• c++17 compliant compiler (clang 7+, gcc 8+)
• python >= 3.8

Dependencies

• nanobind

Instalation

Via ssh (recommended):

pip install git+git://github.com/tbrekalo/mini.git@master

Via https (if you do not have GitHub ssh configured):

pip install git+https://github.com/tbrekalo/mini.git@master

Usage

from minipy import KMer, minimize, decode_kmer

EG_SEQ =  "AACCTTGGACTACGATCGGGGGRACCCCGAACATCTCCTCTCCCATTCTCCCTCCCCTAGAGATTCATTC" \
          "AACCTTGGACTACGATCGGGGGRACCCCGAACATCTCCTCTCCCATTCTCCCTCCCCTAGAGATTCATTC"

KMER_LEN = 29
WIN_LEN = 9

minimizers = minimize(EG_SEQ, KMER_LEN, WIN_LEN)
for m in minimizers:
  print(f'{decode_kmer(m, KMER_LEN)}, {m.value()}, {m.position()}, {m.strand()}')