ViFi | identifying viral integration and fusion mRNA reads | Genomics library

by namphuon Python Version: Current License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | ViFi Summary

ViFi is a Python library typically used in Manufacturing, Utilities, Energy, Utilities, Artificial Intelligence, Genomics, Tensorflow applications. ViFi has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. However ViFi build file is not available. You can download it from GitHub.

ViFi is a tool for detecting viral integration and fusion mRNA sequences from Next Generation Sequencing data. Unlike standard approaches that use reference-based read mapping for identification of viral reads, ViFi uses both reference-based read mapping and a phylogenetic-based approach to identify viral reads. ViFi also incorporates mappability scores of the reads to filter out false positive integration detection. The end result is a tool that can accurately and precisely detect integrated viruses, even if the viruses are highly mutated or novel strains. ViFi is currently in alpha testing, is is constantly undergoing revisions. High on the priority list is an easier installation process, as well as improve user interface. Please report any problems/bugs to Nam Nguyen (ndn006@eng.ucsd.edu) so that ViFi can be improved and problems can be quickly corrected. Due to major issues with incompatibilities between versions of Pysam and Samtools, Python versions, as well as issues with software compatibility between different platforms, we highly recommend that users discontinue the use the Python version of ViFi, and instead, use the Dockerized version of ViFi. The Dockerized version is platform independent and only requires Python (either version 2.7 or 3.0) and Docker to be installed, and no other software package is needed. We outline below how to set up and install the Dockerized version, and how to run the Dockerized version. In addition, we include a [Tutorial] for all the different options within ViFi below. We will include instructures on how to run ViFi from the source code, but again, strongly discourage against this usage.

Support

Quality

Security

License

Reuse

Support

ViFi has a low active ecosystem.

It has 25 star(s) with 12 fork(s). There are 4 watchers for this library.

It had no major release in the last 6 months.

There are 9 open issues and 14 have been closed. On average issues are closed in 58 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of ViFi is current.

Quality

ViFi has 0 bugs and 0 code smells.

Security

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

ViFi code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ViFi is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

ViFi releases are not available. You will need to build from source code and install.

ViFi has no build file. You will be need to create the build yourself to build the component from source.

Installation instructions, examples and code snippets are available.

ViFi saves you 623 person hours of effort in developing the same functionality from scratch.

It has 1450 lines of code, 52 functions and 7 files.

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

Top functions reviewed by kandi - BETA

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

get rep_content
Find a set of true breakpoint ranges .
Calculate the offset of each chromosome .
Run Nhmmer pipeline .
Decompose a tree .
Build hms .
Find the largest subset of clist
Read Nhmmer result from file
Prepare sequences that are mapped to HMC .
Load the exons file

Get all kandi verified functions for this library.

ViFi Key Features

No Key Features are available at this moment for ViFi.

ViFi Examples and Code Snippets

No Code Snippets are available at this moment for ViFi.

Community Discussions

Trending Discussions on ViFi

Highcharts: zero-align y-axes angular 6

QUESTION

Highcharts: zero-align y-axes angular 6

Asked 2019-Jan-23 at 14:54

I need to implement a chart like in this link: highchart-image

So i found a plugin in highchart, i think is usefull to use it:

http://highchartsweb.vifi.ee/plugin-registry/single/42/Zero-align%20y-axes

I use the file who is responsible for the alignement with name 'tick_positioner.js' and i add it to my angular application.

...

ANSWER

Answered 2019-Jan-23 at 14:54

To create such type of chart, you do not need to use zero-align y-axes plugin:

Source https://stackoverflow.com/questions/54329642

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

Vulnerabilities

No vulnerabilities reported

Install ViFi

We provide instructions for preparing ViFi to be used for Docker below. If Perl is installed, the setup.sh script can be run that will automatically perform steps 3-7. Note that ViFi requires a large amount of diskspace to setup and run (10 Gb) due to the large size of the initial reference repositories. Run steps 3-7 are only necessary if Perl is not installed on the machine or on Windows machine. If Perl is on the machine, then setup_linux_mac.sh can be run to automatically set up ViFi (see to Step 2).
Install Dependencies:
Python (2.7 or 3.0; instructions for 2.7 is shown)
Docker (https://docs.docker.com/install/)
Download and run setup.sh (If Perl is installed and on Mac/Linux system). Running this script will automatically download ViFi from GitHub, automatically download the repositories from Google Drive, pull the latest ViFi docker image, set all the environmental variables for ViFi, build the BWA index for hg19+HPV via Docker, and run a test run of ViFi via Docker. It can take up to an hour for the full set of tests to complete and run. Make sure you have at least 10 Gb of space free for the process to complete.
Clone the ViFi repository
Set the ViFi directory and include the python source to your Python path
Download the data repositories: While we include some annotations, we are unable to host some large files in the git repository. These may be downloaded from https://drive.google.com/open?id=0ByYcg0axX7udUDRxcTdZZkg0X1k. Thanks to Peter Ulz for noticing incorrect link earlier.
Download the HMM models: We have pre-build HMM models for HPV and HBV. They can be downloaded from https://drive.google.com/open?id=0Bzp6XgpBhhghSTNMd3RWS2VsVXM.
Build a BWA index on the reference sequences from human+viral sequences: We show an example of building an index of human+viral sequences using Hg19 and HPV and HBV below. However any reference organism+viral family could be used.
We provide instructions for installing ViFi on Linux below.
ViFi download (if you have not already cloned this source code):
Install Dependencies: Python 2.7 sudo dnf install python2 Pysam verion 0.9.0 or higher (https://github.com/pysam-developers/pysam): sudo pip install pysam Samtools 1.3.1 or higher (www.htslib.org/) sudo apt-get install samtools BWA 0.7.15 or higher (bio-bwa.sourceforge.net/) sudo apt-get install bwa Install HMMER v3.1b2 and have it on the path (http://hmmer.org/) sudo apt-get install hmmer
Set the ViFi directory and include the python source to your Python path
Download the data repositories: While we include some annotations, we are unable to host some large files in the git repository. These may be downloaded from https://drive.google.com/open?id=0ByYcg0axX7udUDRxcTdZZkg0X1k. Thanks to Peter Ulz for noticing incorrect link earlier.
Download the HMM models: We have pre-build HMM models for HPV and HBV. They can be downloaded from https://drive.google.com/open?id=0Bzp6XgpBhhghSTNMd3RWS2VsVXM.
Build a BWA index on the reference sequences from human+viral sequences: We show an example of building an index of human+viral sequences using Hg19 and HPV and HBV below. However any reference organism+viral family could be used.

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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