Skip to main content

Software package for simulating and analyzing microhaplotype sequence data

Project description

MicroHapulator build status Test coverage Platform support install with bioconda BSD licensed

MicroHapulator

Daniel Standage, 2018-2019
https://github.com/bioforensics/microhapulator

MicroHapulator is a package for analyzing and interpreting microhaplotype sequence data for forensic analysis. It provides tools for genotyping as well as deterministic and probabilistic interpretation of simple and complex samples. It also provides tools for constructing mock genotypes and simulating MPS sequencing of single- and multiple-contributor samples. MicroHapulator relies on microhap marker definitions and population allele frequencies from MicroHapDB and the MPS error models included with InSilicoSeq.

Installation

Installation with bioconda is recommended.

conda install -c bioconda microhapulator

NOTE: If you'd prefer to install with pip, see .travis.yml and setup.py for hints.

Interactive demo

Click the badge below to launch a quick interactive demo of MicroHapulator.

Binder

Usage

usage: mhpl8r [-h] [-v] [-l F] [--tee] subcmd ...

≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠
  __  __ _            _  _                _      _
 |  \/  (_)__ _ _ ___| || |__ _ _ __ _  _| |__ _| |_ ___ _ _
 | |\/| | / _| '_/ _ \ __ / _` | '_ \ || | / _` |  _/ _ \ '_|
 |_|  |_|_\__|_| \___/_||_\__,_| .__/\_,_|_\__,_|\__\___/_|
                               |_|
≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠≠
Invoke `mhpl8r <subcmd> --help` and replace `<subcmd>` with one of the
subcommands listed below to see instructions for that operation.

Subcommands:
  subcmd             contain, contrib, diff, dist, mix, prob, seq, sim, type,
                     unite

Global arguments:
  -h, --help         show this help message and exit
  -v, --version      show program's version number and exit
  -l F, --logfile F  log file for diagnostic messages, warnings, and errors
  --tee              write diagnostic output to logfile AND terminal (stderr)

Contributing

We welcome contributions from the community! Feel free to ask questions, make suggestions, or report bugs using the issue tracker. If you are interested in submitting patches, docs/DEVEL.md contains a few suggestions for a development setup. All contributors are expected to abide by the project's Code of Conduct.

Project details


Release history Release notifications

This version

0.4.1

Download files

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

Files for microhapulator, version 0.4.1
Filename, size File type Python version Upload date Hashes
Filename, size microhapulator-0.4.1.tar.gz (2.9 MB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page