Skip to main content

No project description provided

Project description

pyseq-align

Python interface for the seq-align C library, written by Isaac Turner (@noporpoise).

Installation

pip install pyseq-align

To install directly from GitHub,

git clone https://github.com/Lioscro/pyseq-align.git --recursive
cd pyseq-align
pip install .

Usage

Two alignment algorithms are provided: Needleman-Wunsch and Smith-Waterman.

from pyseq_align import NeedlemanWunsch

nw = NeedlemanWunsch()
al = nw.align('ACGT', 'ACGTC')
print(al.result_a)  # ACGT-
print(al.result_b)  # ACGTC
print(al.score)
from pyseq_align import SmithWaterman

sw = SmithWaterman()
als = sw.align('ACGT', 'ACGTC')  # unlike above, this is a list of Alignment's
for al in als:
    print(al.result_a, al.pos_a)  # ACGT, 0
    print(al.result_b, al.pos_b)  # ACGT, 0
    print(al.score)

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pyseq-align-1.0.2.tar.gz (272.3 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page