Sequence Python Packages

pygrinder

PyGrinder: a Python toolkit for grinding data beans into the incomplete for real-world data simulation by introducing missing values with different missingness patterns, including MCAR (complete at random), MAR (at random), MNAR (not at random), sub sequence missing, and block missing

pyfastx

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

mdiff

Package for finding difference between two input sequences with ability to detect sequence elements displacements.

sequenzo

A fast, scalable, and intuitive Python package in sequence analysis.

django-generate-series

Use Postgres' generate_series to create sequences with Django's ORM

orange3-timeseries

🍊 :chart_with_upwards_trend: Orange add-on for analyzing, visualizing, manipulating, and forecasting time series data.

pypynum

PyPyNum is a versatile Python math lib. It features modules for math, data analysis, arrays, crypto, physics, RNG, data proc, stats, eq solving, image proc, interp, matrix calc, and high-prec math. Designed for scientific computing, data science, and ML, it offers efficient, general-purpose tools.

seqlike

Unified biological sequence manipulation in Python

ring-seq-py

A Pythonic class for sequences considered circular

cstag

Python module to manipulate and visualize minimap2's cs tag

numpypy

PyPyNum is a versatile Python math lib. It features modules for math, data analysis, arrays, crypto, physics, RNG, data proc, stats, eq solving, image proc, interp, matrix calc, and high-prec math. Designed for scientific computing, data science, and ML, it offers efficient, general-purpose tools.

quicked

QuickEd is a high-performance exact sequence alignment based on the bound-and-align paradigm.

bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

bluewhale3-timeseries

🍊 :chart_with_upwards_trend: Orange add-on for analyzing, visualizing, manipulating, and forecasting time series data.

mutalyzer-algebra

A Boolean Algebra for Genetic Variants

streq

🧬 Python utilities for working with nucleotide sequence strings.

smof

Explore and analyze biological sequence data

camina

Flexible, lightweight, extensible, easy-to-use data structures for Python

perf-ssr

PERF is an exhaustive repeat finder

a-pandas-ex-sequence-search

Sequence / string search with NumPy in pandas DataFrames

sars2seq

A Python library and command-line scripts for working with SARS-CoV-2 sequences

npsearchsequence

Sequence / string search with NumPy

seq-json-schema

Standardized JSON Schema for authoring multi-mission sequences.

pycorruptor

PyGrinder: a Python toolkit for grinding data beans into the incomplete for real-world data simulation by introducing missing values with different missingness patterns, including MCAR (complete at random), MAR (at random), MNAR (not at random), sub sequence missing, and block missing