vampire | Deep generative models for TCR sequences | Machine Learning library

by matsengrp Python Version: 0.2.0 License: Apache-2.0

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

kandi X-RAY | vampire Summary

vampire is a Python library typically used in Artificial Intelligence, Machine Learning, Deep Learning, Tensorflow applications. vampire 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.

This is a package to fit and test variational autoencoder (VAE) models for T cell receptor sequences. It is described in the paper Deep generative models for T cell receptor protein sequences by Kristian Davidsen, Branden J Olson, William S DeWitt III, Jean Feng, Elias Harkins, Philip Bradley and Frederick A Matsen IV.

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Quality

Security

License

Reuse

Support

vampire has a low active ecosystem.

It has 13 star(s) with 3 fork(s). There are 7 watchers for this library.

It had no major release in the last 12 months.

There are 8 open issues and 63 have been closed. On average issues are closed in 38 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of vampire is 0.2.0

Quality

vampire has 0 bugs and 0 code smells.

Security

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

vampire code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

vampire 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

vampire 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.

It has 3101 lines of code, 225 functions and 22 files.

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

Top functions reviewed by kandi - BETA

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

Return a dict containing the command line interface
Create a ConfigParser object from root
Get the project root directory
Extract the version information
Execute local command
Translate paths to destination
Create the versioneer config file
Install versioneer
Build a function to build a model
Returns the highest germline AaaA
Compute the contiguous contiguous match counts for each residue
Return a cluster execution string
Preprocess a tsv file
Deduplicate duplicates on vjcdr3
Evaluate TCRVAE
Compares TCRVAE
Convert unpacked DNA sequences to onehot residue
Calculate the germline sum of inputs
Calculate the variance of a test case
Merge PSC data into a single dataframe
Extract version information from the VCS
Splits the training and test files
Runs the TCRVIAE
Scans the setup py py and returns a boolean indicating whether it is missing
Train a TCRVVA
Generates a sample data set from a selected column

Get all kandi verified functions for this library.

vampire Key Features

No Key Features are available at this moment for vampire.

vampire Examples and Code Snippets

No Code Snippets are available at this moment for vampire.

Community Discussions

Trending Discussions on vampire

Get data from pandas on specifics string

How to set text from encapsulated variable

How do I remove the

Elements not getting hided on button click

Python Rich: Emojis not showing

Modal window not appearing on click

findOneReplace replacment issue

I can't align the image images on the html page, how can I do it?

docker wordpress + nginx returning empty response on curl without headers

How to double a value of private int type field?

QUESTION

Get data from pandas on specifics string

Asked 2022-Apr-16 at 02:48

So here is my code.

...

ANSWER

Answered 2022-Apr-16 at 02:48

import pandas as pd

data = pd.read_csv('cast.csv')
data_2 = data[data['type'] == 'actor']
output = data_2[data['name'].str.startswith('Aaron')]
print(output)

Source https://stackoverflow.com/questions/71890633

QUESTION

How to set text from encapsulated variable

Asked 2022-Mar-12 at 16:06

I have placed this code in a new class

...

ANSWER

Answered 2022-Mar-12 at 10:43

Custom constructor is not properly initialized. When call Monster vampire = new Monster("Vampire", 2000, 300, 25); no values are set, so obvious null:string and 0:numbers returns (java default initializers).

Adapt with:

Source https://stackoverflow.com/questions/71448790

QUESTION

How do I remove the

Asked 2022-Mar-11 at 16:53

So, right now, what I'm trying to do is that I'm trying to scrape a table from rottentomatoes.com and but every time I run the code, I'm facing an issue that it just prints

This is my code so far:

...

ANSWER

Answered 2022-Mar-10 at 21:12

Reading tables via pandas.read_html() as provided by @F.Hoque would probably the leaner approache but you can also get your results with BeautifulSoup only.

Iterate over all of the

tags.text.get_text()

Source https://stackoverflow.com/questions/71430097

QUESTION

Elements not getting hided on button click

Asked 2022-Mar-02 at 07:08

I have added show failures only button in report and trying to make it work so that when show failures is clicked it only shows failure cases. But the button is not working as expected. The control goes to the function but the intended functionality is not working as expected. Please help in hiding the pass cases when this show failure button is clicked.

...

ANSWER

Answered 2022-Mar-02 at 06:00

Add this css style to hide pass cases:

Source https://stackoverflow.com/questions/71317848

QUESTION

Python Rich: Emojis not showing

Asked 2022-Feb-21 at 11:54

from rich import print
from rich.console import Console
console = Console()


#example 1
print("Hello, [bold magenta]World[/bold magenta]!", ":vampire:", locals())

#example 2
console = Console()
print("Hello, [bold magenta]World[/bold magenta]!", "😎")
console.print("Hello", "World!", style="bold red")

#example 3
print(f"I wonder what this looks like 1 + 1 = {1 + 1}")
print({"a": [1, 2, 3], "b" : {"c" : 1}})


#example 4
console.print("This is some text.")
console.print("This is some text.", style="bold")
console.print("This is some text.", style="bold underline")
console.print("This is some text.", style="bold underline red")
console.print("This is some text.", style="bold underline red on black")
 
#example 5
console.print(":thumbs_up: File downloaded!")

input("")

...

ANSWER

Answered 2022-Feb-21 at 11:54

The classic windows console doesn't have good support for emoji. If you install the new Windows Terminal you will find your emojis will appear as expected.

Source https://stackoverflow.com/questions/71205271

QUESTION

Modal window not appearing on click

Asked 2022-Feb-07 at 18:18

I'm new to Bootstrap and jQuery and I'm trying to integrate a modal window in my sales website. I copied the modal code from https://getbootstrap.com/docs/4.3/components/modal/ to get a test visualization of how it would look in my project; the only problem is that whenever I click the modal button nothing appears. I heard that this could be an issue with jQuery not being loaded in my code but I don't know how to do this or if it is an issue to begin with. Here is my code:

html

...

ANSWER

Answered 2022-Feb-07 at 18:18

You have imported only the CSS of Bootstrap 4.

The modal uses also Javascript.

Therefore, you need to import the JS of Bootstrap 4 along with jQuery and Popper.

Add the following lines to your code, before the import of your project's js file.

Source https://stackoverflow.com/questions/71023274

QUESTION

findOneReplace replacment issue

Asked 2022-Jan-29 at 13:02

I want to find a document in my db and replace it with a document that has a new name and new key.

Here is my Schema

...

ANSWER

Answered 2022-Jan-29 at 13:02

There are two issues that I can see.

First, you should pass null as the third argument in your findOneAndReplace call. This will set the options to null and should get your code running. This is in my opinion a strange behavior of mongoose.

Source https://stackoverflow.com/questions/70905225

QUESTION

I can't align the image images on the html page, how can I do it?

Asked 2021-Dec-03 at 10:03

I have 2 div fields in my html page. In each field, there are 5 image images that I have listed sideways. I have 5 images side by side in the div just below. But I couldn't get it to line up. My frontend knowledge is not good, how can I do it?

Page image:

As you can see, they do not stand in line, the images are above and below. How do I get it to stay in line?

Html code:

...

ANSWER

Answered 2021-Dec-03 at 06:00

add fix width to each item .items a{width:130px;} to specify column size and look perfect

Source https://stackoverflow.com/questions/70210064

QUESTION

docker wordpress + nginx returning empty response on curl without headers

Asked 2021-Nov-17 at 16:04

I have a wordpress+nginx in a docker container that is working perfectly through the browser, but when I try to send an http request via curl without headers the response is always empty

...

ANSWER

Answered 2021-Nov-17 at 16:04

This has nothing to do with docker or wordpress or something else.
It is your nginx-configuration solely that rejecting the request:

You have Curl in your http-agent comparison in nginx-server.conf:

Source https://stackoverflow.com/questions/69915359

QUESTION

How to double a value of private int type field?

Asked 2021-Nov-07 at 21:30

This is the code of method takeDamage in the class Enemy which is a superclass of class Vampire.

...

ANSWER

Answered 2021-Nov-07 at 21:30

You need some place where the original hit points are stored.

If your Enemy class doesn't provide this information and you only need it in the Vampire class you could change the Vampire class along these lines:

Source https://stackoverflow.com/questions/69872746

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

Vulnerabilities

No vulnerabilities reported

Install vampire

Conda is the canonical way to prepare your environment and is required run the pipeline, although not strictly a dependency for fitting and using VAEs using this code. These instructions will assume that you have installed Conda. If you want to see the entire environment preparation process process, see the Dockerfile. However, if you simply want to train and use vampire models, you can only execute. This will create a vampire Conda environment which you can enter and use for running vampire. If you also want to be able to compare repertoires using sumrep you will need to run the R installation steps in the Dockerfile. We also provide an install/environment-olga.yml to make a Conda environment in which one can run OLGA.
After setting up your environment (if you followed the steps above you'll need to conda activate vampire), and run. in the repository to install vampire. If you want to use sumrep, see install/test.sh for additional install instructions.