clinvar | repo provides tools to convert ClinVar data

by macarthur-lab Python Version: 2018_02_01-release License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(6)Vulnerabilities Install Support

kandi X-RAY | clinvar Summary

clinvar is a Python library. clinvar has no bugs, it has no vulnerabilities and it has low support. However clinvar build file is not available and it has a Non-SPDX License. You can download it from GitHub.

clinvar has fixed the issues that originally motivated creating this project, so we are now using the clinvar VCFs for our analyses.

Support

Quality

Security

License

Reuse

Support

clinvar has a low active ecosystem.

It has 110 star(s) with 52 fork(s). There are 41 watchers for this library.

It had no major release in the last 12 months.

There are 6 open issues and 36 have been closed. On average issues are closed in 57 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of clinvar is 2018_02_01-release

Quality

clinvar has no bugs reported.

Security

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

License

clinvar has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

clinvar releases are available to install and integrate.

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

Installation instructions are not available. Examples and code snippets are available.

Top functions reviewed by kandi - BETA

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

Parse the clinvar tree
Remove newlines and tabs
Convert a table to a VCF file
Open a file - like object
Group alleles by allele
Group alleles from two variants
Download files from remote
Returns the last time of a remote file
Extract column values from a single VCF file
Return a handle object

Get all kandi verified functions for this library.

clinvar Key Features

No Key Features are available at this moment for clinvar.

clinvar Examples and Code Snippets

No Code Snippets are available at this moment for clinvar.

Community Discussions

Trending Discussions on clinvar

Missing bootstrap table Icons

How to delete grepl-unmatched column values in R

parsing xml content using R to extract the title information

How to turn a list into a datafame (matched by ID)?

Using bash functions in snakemake

Looking for how to use separate() with multiple separators in R (ClinVar variant data dealing)

QUESTION

Missing bootstrap table Icons

Asked 2021-Feb-27 at 16:48

I'm using Bootstrap and Bootstrap-table, but can't get the icons to show. I've double checked to make sure that my versions are correct, however regardless the icons for print, sort etc are not showing at the top of the table. When I copy the code into the bootstrap-table online editor, the multi sort shows but not the other buttons. This phenomenon is platform independent (occurs in chrome, firefox and safari).

The Problem (Notice the lack of icons)

What I should be seeing

My HTML Header

...

ANSWER

Answered 2021-Feb-27 at 16:48

I was dealing with this exact issue. In my case i was missing the link to fontawesome where they are pulling the icons:

link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.6.3/css/all.css"

Source https://stackoverflow.com/questions/66374929

QUESTION

How to delete grepl-unmatched column values in R

Asked 2020-Jul-09 at 19:43

I have a dataframe called mydf. I want to look for the presence of c.change values in Clinvar_Type. If present, I want to delete everything in grepl("Clinvar, colnames(mydf)).

This is my data:

...

ANSWER

Answered 2020-Jul-09 at 18:07

Here is a base R solution. (you can replace "" with NA if you prefer).

Source https://stackoverflow.com/questions/62820469

QUESTION

parsing xml content using R to extract the title information

Asked 2020-Jun-09 at 00:47

I have a xml data

...

ANSWER

Answered 2020-Jun-08 at 10:25

Here is my go at things... does that help?

Source https://stackoverflow.com/questions/62259249

QUESTION

How to turn a list into a datafame (matched by ID)?

Asked 2020-Apr-09 at 09:53

I have a list of vectors, and I want to combine these, matched by ID, into a new data frame.

You can recreate my problem using this code:

...

ANSWER

Answered 2020-Apr-09 at 09:43

you can try a tidyverse & purrr approach which combines not only two but also multiple list elements by rowid:

Source https://stackoverflow.com/questions/61117935

QUESTION

Using bash functions in snakemake

Asked 2020-Feb-14 at 15:17

I am trying to download some files with snakemake. The files (http://snpeff.sourceforge.net/SnpSift.html#dbNSFP) I would like to download are on a google site/drive and my usual wget approach does not work. I found a bash function that does the job (https://www.zachpfeffer.com/single-post/wget-a-Google-Drive-file):

...

ANSWER

Answered 2020-Feb-08 at 18:33

You would want to use raw string literal so that snakemake doesn't escape special characters, such as backslash in sed command. For example (notice r in front of shell command):

Source https://stackoverflow.com/questions/60127866

QUESTION

Looking for how to use separate() with multiple separators in R (ClinVar variant data dealing)

Asked 2020-Jan-22 at 02:03

Dear StackOverflow community

I'm a biologist and I'm working with a disease/genetic variants from ClinVar official database. My aim is to extract all gene names, transcripts and variants from this list.

ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2020-01.xml.gz

However, ClinVar offers the information I need in a single column called "Name". (I've separated some of the values with different results that I want to deal with in the example in the table below:)

...

ANSWER

Answered 2020-Jan-22 at 02:03

I was trying to do this with one single extract/separate but I couldn't come up which would give the exact expected output. So here is an attempt breaking it down into separate steps using str_extract from stringr and sub from base R.

Source https://stackoverflow.com/questions/59850270

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

Vulnerabilities

No vulnerabilities reported

Install clinvar

You can download it from GitHub.
You can use clinvar like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

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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