sigalign 0.1.0

No project description provided

SigAlign for python

Requirements

• python >=3.7

Install

pip install sigalign

Usage Example

from sigalign import SequenceStorage, Reference, Aligner

# 1. Define `SequenceStorage`
ss = SequenceStorage()
ss.add_record("record_1", "ACACAGATCGCAAACTCACAATTGTATTTCTTTGCCACCTGGGCATATACTTTTTGCGCCCCCTCATTTA")
ss.add_record("record_2", "TCTGGGGCCATTGTATTTCTTTGCCAGCTGGGGCATATACTTTTTCCGCCCCCTCATTTACGCTCATCAC")

# 2. Build `Reference`
reference = Reference(
    ss,
    klt_size = 2,
    sas_ratio = 2,
    comp_block = True,
)

# 3. Make `Aligner`
aligner = Aligner(
    4,
    6,
    2,
    50,
    0.2,
    is_local_mode = True,
)

# 4. Perform alignment
query = "CAAACTCACAATTGTATTTCTTTGCCAGCTGGGCATATACTTTTTCCGCCCCCTCATTTAACTTCTTGGA"
result = aligner.align_query(reference, query)

# 5. Print result
import json
json.loads(result.to_json())

import pandas as pd
df = pd.DataFrame(
    result.to_2d_array(),
    columns = [
        'index', 'label', 'penalty', 'length',
        'qstart', 'qend', 'rstart', 'rend', 'operations',
    ]
)

Build manually

• Use maturin as backend

  pip install maturin
  maturin develop