igv-reports | Python application to generate self

by igvteam Python Version: 1.12.0 License: MIT

X-Ray Key Features Code Snippets(2)Community Discussions Vulnerabilities Install Support

kandi X-RAY | igv-reports Summary

igv-reports is a Python library. igv-reports has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. However igv-reports has 7 bugs. You can install using 'pip install igv-reports' or download it from GitHub, PyPI.

Python application to generate self-contained igv.js pages that can be opened within a browser with "file" protocol.

Support

Quality

Security

License

Reuse

Support

igv-reports has a low active ecosystem.

It has 227 star(s) with 40 fork(s). There are 14 watchers for this library.

There were 2 major release(s) in the last 12 months.

There are 7 open issues and 43 have been closed. On average issues are closed in 227 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of igv-reports is 1.12.0

Quality

igv-reports has 7 bugs (0 blocker, 0 critical, 7 major, 0 minor) and 46 code smells.

Security

igv-reports has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

igv-reports code analysis shows 0 unresolved vulnerabilities.

There are 5 security hotspots that need review.

License

igv-reports 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

igv-reports releases are available to install and integrate.

Deployable package is available in PyPI.

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

Installation instructions, examples and code snippets are available.

igv-reports saves you 628 person hours of effort in developing the same functionality from scratch.

It has 1900 lines of code, 82 functions and 29 files.

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

Top functions reviewed by kandi - BETA

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

Create a report from the given arguments
Fetch data from the vcf file
Slice the fasta sequence
Get a genome by ID
Parse a locus region
Convert to JSON
Render an ID
Decode an annotation
Normalize a JSON array
Return a dictionary with track information
Get track type
Return the name of a filename
Return a feature reader instance
Return a FeatureReader instance
Infer the format of a file
Fetch data from the file
Fetch data from file
Returns a list of features that match the given region
Return the name of a chrname
Convert a file to a data URI
Compute the data URI
Load a genome by ID
Merge multiple regions
Parse a locus region

Get all kandi verified functions for this library.

igv-reports Key Features

No Key Features are available at this moment for igv-reports.

igv-reports Examples and Code Snippets

igv-reports,Examples

Python

Lines of Code : 16

License : Permissive (MIT)

Copy


create_report examples/variants/variants.vcf.gz https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa --ideogram examples/variants/cytoBandIdeo.txt --flanking 1000 --info-columns GENE TISSUE TUMOR COSMIC_ID GENE SOMATIC --tracks e

igv-reports,Installation

Python

Lines of Code : 7

License : Permissive (MIT)

Copy

conda create -n myenv python=3.7.1
conda install -n myenv pip
conda activate myenv

pip install igv-reports

conda config --add channels r
conda config --add channels bioconda
conda install pysam

Community Discussions

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

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

Vulnerabilities

No vulnerabilities reported

Install igv-reports

igv-reports requires Python 3.6 or greater and pip. As with all Python projects, use of a virtual environment is recommended. Instructions for creating a virtual environment using conda follow. 1. Install Anaconda from https://docs.anaconda.com/anaconda/. 2. Create a virtual environment. igv-reports requires the package pysam which should be installed automatically. However on OSX this sometimes fails due to missing dependent libraries. This can be fixed following the procedure below, from the pysam docs; "The recommended way to install pysam is through conda/bioconda. This will install pysam from the bioconda channel and automatically makes sure that dependencies are installed. Also, compilation flags will be set automatically, which will potentially save a lot of trouble on OS X.".

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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