A Python3 module for fast & easy sequence comparison.
Project description
Welcome to scalabis
A Python3 module for fast & easy sequence comparison
scalabis is built on numba and numpy, taking advantage of JIT compiled functions for speedy mismatched sequence comparisons.
Instructions
Install scalabis using pip:
pip install scalabis
Import it as any other python module:
import scalabis as sc
Usage examples. See help(function) after import for more use details:
sequence1 = "pihton"
sequence2 = "Hello there, this is a test for a fast & easy mismatch matching python module. Allegedly, it is efficient"
count by how many mismatches 2 same lenght sequences diverge:
sc.mismatch_counter(sequence1,sequence2)
find one sequence in another, with mismatches. return_template=True returns
sc.find(sequence1,sequence2,mismatch=1)
without return in a class
sc.find(sequence1,sequence2,mismatch=2,dict_return=False)
compare two sequences, searching from the search sequence from a specified starting point (default=0), returning the full aligned matrix whrere mismatches are 1, and matches are 0. Mismatches are the total mismatches in the compared matrix
sc.comparefromfound(sequence1,sequence2,mismatch=0,start=0,dict_return=True)
compare two sequences, returning all the locations in which they differ
sc.compareandlocate(start=0,search=sequence1,template=sequence2)
compare two sequences, returning the full aligned matrix. starting point can be specified
sc.compare(search=sequence1,template=sequence2,start=0,dict_return=False)
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