hlama | Simple matching of HTS samples based on HLA

by bihealth Python Version: v0.3.1 License: MIT

X-Ray Key Features Code Snippets Community Discussions Vulnerabilities Install Support

kandi X-RAY | hlama Summary

hlama is a Python library. hlama has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

Simple matching of HTS samples based on HLA typing

Support

Quality

Security

License

Reuse

Support

hlama has a low active ecosystem.

It has 12 star(s) with 2 fork(s). There are 5 watchers for this library.

It had no major release in the last 12 months.

hlama has no issues reported. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of hlama is v0.3.1

Quality

hlama has 0 bugs and 0 code smells.

Security

hlama has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

hlama code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

hlama is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

hlama releases are available to install and integrate.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

hlama saves you 323 person hours of effort in developing the same functionality from scratch.

It has 775 lines of code, 78 functions and 10 files.

It has medium code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed hlama and discovered the below as its top functions. This is intended to give you an instant insight into hlama implemented functionality, and help decide if they suit your requirements.

Check consistency of HLA calls
Check consistency of two calls
Return a string representation of the given precision
Parse HLAType string
Load HLA calls
Parse a pedigree file
Run tests
Create output directory
Check the info
Create a symlink link to the snakefile
Create the JSON representation of the pedigree
Determine the mode of a list of files
Check that all FASTQ files are present
Locates a file at the specified path
Verify that all FASTQ files are present
Return the JSON representation of the HLA checks
Load configuration
Load a configuration file
Parse a Cohort from a file
Return True if other is equal to other
Return True if two strings are equal

Get all kandi verified functions for this library.

hlama Key Features

No Key Features are available at this moment for hlama.

hlama Examples and Code Snippets

No Code Snippets are available at this moment for hlama.

Community Discussions

No Community Discussions are available at this moment for hlama.Refer to stack overflow page for discussions.

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install hlama

Note that OptiType is a Python 2 program while HLA-MA is a Python 3 program. We recommend installing the dependencies OptiType, Yara, and RazerS3 using Bioconda. Futher, you can now also install HLA-MA into the same conda environment. You can skip this step if you have already installed the prerequisites and placed them in your $PATH. The following commands will install Miniconda2 (for Python 2) in ~/miniconda2. Activate Miniconda 2 installation by adding bin path, then add R and Bioconda channels.

Support

Q: Should I use single-end data or paired-end data? A: Both can be used but we observe much better precision in OptiType with paired-end data. Q: The image you are using is an alpaca! A: That's true but lamas and alpacas are closely related.

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