varcode | Library for manipulating genomic variants | Genomics library

by openvax Python Version: 1.2.0 License: Apache-2.0

X-Ray Key Features Code Snippets(1)Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | varcode Summary

varcode is a Python library typically used in Artificial Intelligence, Genomics applications. varcode has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install varcode' or download it from GitHub, PyPI.

Varcode is a library for working with genomic variant data in Python and predicting the impact of those variants on protein sequences.

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Security

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Support

varcode has a low active ecosystem.

It has 66 star(s) with 21 fork(s). There are 11 watchers for this library.

There were 1 major release(s) in the last 6 months.

There are 30 open issues and 100 have been closed. On average issues are closed in 286 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of varcode is 1.2.0

Quality

varcode has 0 bugs and 0 code smells.

Security

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

varcode code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

varcode is licensed under the Apache-2.0 License. This license is Permissive.

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

Reuse

varcode 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.

varcode saves you 2699 person hours of effort in developing the same functionality from scratch.

It has 5850 lines of code, 408 functions and 56 files.

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

Top functions reviewed by kandi - BETA

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

Load a MAF file
Try to infer the genome from the given string
Infer the genome from a reference name
Infer a reference name based on the reference name
Create a VariantCollection from command line arguments
Combine variants and other collections
Download and install reference data
Load data from a MAF file
The list of gene names in this loci
Dictionary of gene counts
List of gene ids associated with this locus
Keep effects on each transcript
Filter effects on protein coding genes
Return dictionary of gene counts
List of genes associated with this locus
Return the gene_id of an effect
Returns the top priority effect
Filter effects on protein coding transcripts
Create an argument parser
Merge ensembl aliases
Return a human - readable string representation of the results
Return the top expression that matches the given expression levels
Return the effect collection of variants in this variant collection
Return the sort key for a single gene effect
Return a string representation of the variant
Select the effect between an ExonicSpliceSite and the alternate effect

Get all kandi verified functions for this library.

varcode Key Features

No Key Features are available at this moment for varcode.

varcode Examples and Code Snippets

Varcode,Example

Python

Lines of Code : 48

License : Permissive (Apache-2.0)

Copy

import varcode

# Load TCGA MAF containing variants from their
variants = varcode.load_maf("tcga-ovarian-cancer-variants.maf")

print(variants)
### 
###  -- Variant(contig=1, start=69538, ref=G, alt=A, genome=GRCh37)
###  -- Variant(contig=1, start=8

Community Discussions

Trending Discussions on varcode

Compare the unique code numbers and highest rates among the unique ID number in two sheets

C# Dictionary updates by itself

Java JDBC executeUpdate arraycopy: length -1434 is negative

Build a view from a query

Removing a custom (second) class from a dataset/variable

Getting the labels of the column names (hmisc)

Using a list / dataframe / vector to assign labels to column names of a dataframe with Hmisc

Dataframe does not correctly reshape

Transform several XML elements, identified by their attributes, into a complex one

AspxGridview Add new row and retain last row value

QUESTION

Compare the unique code numbers and highest rates among the unique ID number in two sheets

Asked 2021-Apr-04 at 17:09

There are two sheets Kevin and James. Both the sheets have unique code numbers and rates. The code below is to find out the unique code numbers in both sheets and the highest rates among the unique codes and result will be in a separate Summary sheet. Could you let me know where the code is wrong.

...

ANSWER

Answered 2021-Apr-04 at 17:09

Don't use Select and ActiveCell refer to the cell you want with Cells(rowno,column)

Source https://stackoverflow.com/questions/66934519

QUESTION

C# Dictionary updates by itself

Asked 2021-Mar-05 at 12:38

I'll try to resume everything as much as possible:

I have a class that creates a dictionary (let's call it secondary dictionary) with the initial values of some of the elements of another dictionary, (for simplicity, let's call it the main dictionary and this class does this only once) and then a thread that checks every x miliseconds against this main dictionary, that's being regularly updated every y miliseconds, for any changes on the elements that where stored in the initialization phase.

My problem is, that when I want to compare the values of element1 in the main dictionary against the value of element1 in the secondary dictionary, they're always the same, (I undersatnd that, until the main dictionary is nnot updated, both values will be the same, but when the main dictionary gets updated, so does the second, immediately, without me doing anything)

I've tried ConcurrentDictionaries, using locks, a combination of boths, creating a new element in the initialize functions instead of passing it directly, but nothing seems to work

...

ANSWER

Answered 2021-Mar-05 at 12:38

As fildor already said, you have one object and two references to it. To simplify your problem I created a short sample:

Source https://stackoverflow.com/questions/66492170

QUESTION

Java JDBC executeUpdate arraycopy: length -1434 is negative

Asked 2020-Apr-30 at 09:58

I've got problem with calling stored procedure in DB2. If i run it without java, it'll work fine. Can someone help me with that? The problem does not depend on message variable and i can't get whats wrong with it.

Here's the code:

...

ANSWER

Answered 2020-Apr-30 at 09:58

This looks to be a known issue - you need to upgrade to the latest DB2 JDBC driver.

Source https://stackoverflow.com/questions/61520142

QUESTION

Build a view from a query

Asked 2019-Dec-16 at 15:22

I want to build a view from a T-SQL query. Here is the query:

...

ANSWER

Answered 2019-Dec-16 at 15:22

There are several issues to discuss.

First, there is one very important difference between your query and your view. In your query, you have a known, working join structure. In your view, you immediately interfere with the known, working join structure by using a cross apply. I believe this is breaking the join structure in a way you aren't expecting, and so you don't get your desired results. I would suggest you eliminate the cross apply along with the params CTE. Instead, you could just insert the "params" values directly into the source. So instead of:

Source https://stackoverflow.com/questions/59325795

QUESTION

Removing a custom (second) class from a dataset/variable

Asked 2019-Aug-19 at 10:57

I have been using a class from the hmisc package called haven_labelled (or sometimes just labelled). It purpose is to import the column labels from a Stata .dta dataset. When trying to use plm on a dataframe I got the error:

...

ANSWER

Answered 2019-Aug-19 at 09:46

This solution based on the provided dataset DTp, change labelled and labelled_ch according to your original dataset

Source https://stackoverflow.com/questions/57543054

QUESTION

Getting the labels of the column names (hmisc)

Asked 2018-Aug-28 at 15:09

I have used the Hmisc library to attach labels to column names, which you could do as follows.

example

...

ANSWER

Answered 2018-Aug-28 at 15:09

Here we extract the labels from each column and stack it to a data.frame with two columns

Source https://stackoverflow.com/questions/52060768

QUESTION

Using a list / dataframe / vector to assign labels to column names of a dataframe with Hmisc

Asked 2018-Aug-05 at 08:31

I would like to use the column Variables of a dataframe:

...

ANSWER

Answered 2018-Aug-05 at 08:31

This is a tricky one. So, I will show stepwise what I have tried.

1. Reshaping without label<-()

In a first attempt, I resorted to data.table which I am more acquainted.

Source https://stackoverflow.com/questions/51674973

QUESTION

Dataframe does not correctly reshape

Asked 2018-Aug-03 at 13:11

I have the following dataframe:

...

ANSWER

Answered 2018-Aug-03 at 12:52

I think you went wrong with your selection of columns to gather

Data:

Source https://stackoverflow.com/questions/51672112

QUESTION

Transform several XML elements, identified by their attributes, into a complex one

Asked 2017-Oct-09 at 11:28

I am quite new to XSLT so I could be missing something really obvious.

I have a source XML in this format:

Source:

...

ANSWER

Answered 2017-Oct-09 at 11:21

Try this simple xslt

Source https://stackoverflow.com/questions/46645065

QUESTION

AspxGridview Add new row and retain last row value

Asked 2017-Jul-31 at 08:46

I have a aspxgridview that will allow the user to add new row. What I want to do is to retain the value of last row everytime the new row has been added. I have the Add new row button outside the gridview. Is it possible? Any help would be much appreciated.

Below is what I have so far.

Front-end

...

ANSWER

Answered 2017-Jul-31 at 08:46

Solution: You should Create the empty(Add New) row from client side instead of creating from server side. change the button code in front end like following,

Source https://stackoverflow.com/questions/45408547

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

Vulnerabilities

No vulnerabilities reported

Install varcode

You can install varcode using [pip](https://pip.pypa.io/en/latest/quickstart.html):.

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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