STAG | STAG : Species Tree from All Genes | Genomics library

by davidemms Python Version: 1.0.0 License: GPL-3.0

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

kandi X-RAY | STAG Summary

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

STAG is a method for inferring a species tree from a set of gene trees. It can use gene trees inferred from any gene family that contains all the species under consideration. These gene familes can contain paralogues, co-orthologues, or any number of gene duplcation events, and thus STAG is not limited to analysis of gene trees inferred from sets of one-to-one orthologues. This ability to use paralogous gene families enables the use of substantially more data from which to base species tree inference.

Support

Quality

Security

License

Reuse

Support

STAG has a low active ecosystem.

It has 19 star(s) with 4 fork(s). There are 4 watchers for this library.

It had no major release in the last 12 months.

There are 0 open issues and 2 have been closed. On average issues are closed in 11 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of STAG is 1.0.0

Quality

STAG has 0 bugs and 0 code smells.

Security

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

STAG code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

STAG 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

STAG releases are available to install and integrate.

STAG 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.

STAG saves you 700 person hours of effort in developing the same functionality from scratch.

It has 1619 lines of code, 125 functions and 4 files.

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

Top functions reviewed by kandi - BETA

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

Construct a consensus tree from the given trees
Returns the canonical representation of the feature
Get all the splits from a directory
Invert the QR code
Updates the splits tree
Construct a tree tree
Determines the split of a list of splits
Processes a directory tree
Gets the distance between each node in the tree
Convert a gene name to a species name
Writes phonopy matrix
Runs the GenoFinder
Create an Astral Tree
Infer species tree
Check if fastme is installed
Determines if the given command can run
Creates a new working directory
Returns a directory name
Infer a species tree

Get all kandi verified functions for this library.

STAG Key Features

No Key Features are available at this moment for STAG.

STAG Examples and Code Snippets

No Code Snippets are available at this moment for STAG.

Community Discussions

Trending Discussions on STAG

Nuxt application local development server constantly reloading

Flip a Multiple Columns and multiple rows in table in Snowflake

Beaglebone / Yocto / Kernel configuration

How to replace characters which are not alphanumeric in pyspark sql?

My actionPerformed method(Java) is not working and I have no clue why

Helm Construct dynamic configmap from multiple configuration YAML file

Why mark stag functions are not called here?

Postgres DB URL string from a K8s deployment yaml file

Getting "PKIX path building failed" error while running my selenium client code inside docker container

'Promise' is undefined in IE11

QUESTION

Nuxt application local development server constantly reloading

Asked 2022-Apr-03 at 10:40

I have a Nuxt ^2.15.8 application which is constantly reloading after I run yarn dev.

The console will show a message like ↻ Updated 1647868577626, and then the application is rebuilt, as if I just run yarn dev. This happens constantly over and over, without me doing any changes in the code.

I googled a bit, and found applications like gitkraken might be modifying the content of the .git folder and that could trigger a reload.

So I keep gitkraken closed.

I also added these lines to my nuxt.config.js file:

...

ANSWER

Answered 2022-Apr-03 at 10:40

Update

The actual issue was actually a version bump of ESlint from 1.x.x to 3.x.x. git bisect helped finding out the actual culprit!

Cloning the repo again and reinstalling the dependencies again, fixed all the above mentioned issues while running yarn dev!

Source https://stackoverflow.com/questions/71558358

QUESTION

Flip a Multiple Columns and multiple rows in table in Snowflake

Asked 2022-Mar-14 at 23:11

Unable to pivot multiple columns in snowflake and I would appreciate it if some one can help me:

I basically have the table attached in the screenshot in the left and need to change it to the format in the right. I wonder if pivot can work in this case ?

my current code:

...

ANSWER

Answered 2022-Mar-14 at 23:11

So assuming the SQL you have posted is more like this (with included fake data in a CTE)

Source https://stackoverflow.com/questions/71468128

QUESTION

Beaglebone / Yocto / Kernel configuration

Asked 2022-Feb-23 at 06:33

I want to change Kernel configuration.

I have my own layer created and inside my layer I have a _%.bbappend file which directly targets the recipe linux-ti-staging.bb (link). This recipe builds my kernel:

...

ANSWER

Answered 2022-Feb-14 at 12:45

Your directory structure should be like this

Source https://stackoverflow.com/questions/71111397

QUESTION

How to replace characters which are not alphanumeric in pyspark sql?

Asked 2022-Feb-14 at 15:16

this is my code.

...

ANSWER

Answered 2022-Feb-14 at 15:15

Apply regexp_replace() to the column in your query:

Source https://stackoverflow.com/questions/71113795

QUESTION

My actionPerformed method(Java) is not working and I have no clue why

Asked 2022-Jan-23 at 17:24

Here is my whole program, don't wonder about the words I am using, I am German. Down from l. 95 to l. 103 is the action performed method, (I only did the System.out.println() to see wether it is working or not). I wrote other programs, where I never had any such problems, and I tried so many things, but I did not find the problem, maybe it is a total simple one... So I would appreciate it if you help me!

...

ANSWER

Answered 2022-Jan-23 at 17:24

As the guys mentioned in the comments, you have not added the listener to your component (update button). If you are using a button, you might consider using a MouseListener instead

Source https://stackoverflow.com/questions/70824464

QUESTION

Helm Construct dynamic configmap from multiple configuration YAML file

Asked 2022-Jan-05 at 11:20

I have 2 files as follows:

_config-dev.yaml

...

ANSWER

Answered 2022-Jan-05 at 11:20

my test project

Source https://stackoverflow.com/questions/70546983

QUESTION

Why mark stag functions are not called here?

Asked 2022-Jan-01 at 22:26

I am trying to understand the following behaviour of OCaml Format module and semantic tags.

My code:

...

ANSWER

Answered 2022-Jan-01 at 21:52

This is an interaction between buffering and utop handling of the stdout formatter.

The buffering issue can be seen with

Source https://stackoverflow.com/questions/70550929

QUESTION

Postgres DB URL string from a K8s deployment yaml file

Asked 2021-Nov-01 at 14:33

I am trying to contact from a customized helm chart to a fully managed Postgres service on azure, and then I have to put the url connection string according to the app I want to deploy.

I want to ask which value should be the DATABASE_URL at the helm chart deployment? My situation is the following:

I want to use an external Azure managed PostgreSQL and no the PostgreSQL container that comes with the helm chart. So in consequence, I modified the DATABASE_URL value, given here to connect to the container inside K8s, I've modified in this way:

...

ANSWER

Answered 2021-Oct-29 at 14:29

From what I see this helm chart is poorly written, and badly assumes things i.e. the DATABASE_URL has is build to only properly format a kubernetes posgress helm release and nothing else.

What I would suggest:

Instead of installing this chart on k8s by helm, use helm template functionality to locally render the template.
Edit the exported plain manifest, to match your needs
Go to your Azure DB, and get it ConnectionString, depending on how you mange your secrets in k8s, pass it to the DATABASE_URL environment
Manually apply the manifests

Source https://stackoverflow.com/questions/69770235

QUESTION

Getting "PKIX path building failed" error while running my selenium client code inside docker container

Asked 2021-Oct-15 at 08:04

I am connecting to selenium grid to run my selenium tests. The client code is dockerized using the below dockerfile

...

ANSWER

Answered 2021-Oct-15 at 08:04

I had to convert the crt file to der format first

Source https://stackoverflow.com/questions/69493857

QUESTION

'Promise' is undefined in IE11

Asked 2021-Sep-20 at 02:34

I have used this plugin to create popups in the Divi website I have built: https://wordpress.org/plugins/popups-for-divi/

The popups were not opening in IE because of the padStart() function and I found an alternative to replace the padStart() function using this code:

< script >

...

ANSWER

Answered 2021-Sep-20 at 02:34

I was able to resolve this problem by adding these two lines of code in the Header:

Source https://stackoverflow.com/questions/69240618

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

Vulnerabilities

No vulnerabilities reported

Install STAG

You can download it from GitHub.
You can use STAG 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 .

Find more information at: