ete | Python package for building comparing annotating | Genomics library

by etetoolkit Python Version: 3.1.3 License: GPL-3.0

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

kandi X-RAY | ete Summary

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

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

Support

Quality

Security

License

Reuse

Support

ete has a low active ecosystem.

It has 694 star(s) with 204 fork(s). There are 35 watchers for this library.

It had no major release in the last 12 months.

There are 199 open issues and 280 have been closed. On average issues are closed in 220 days. There are 10 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of ete is 3.1.3

Quality

ete has 0 bugs and 0 code smells.

Security

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

ete code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ete 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

ete releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

Top functions reviewed by kandi - BETA

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

Main function .
Schedule a workflow .
Validate this section .
Perform Robisson Folds algorithm .
Process a single node .
Render a tree .
Render an image .
Saves a scene .
Render a tree .
Returns a decision tree for the given node .

Get all kandi verified functions for this library.

ete Key Features

No Key Features are available at this moment for ete.

ete Examples and Code Snippets

No Code Snippets are available at this moment for ete.

Community Discussions

Trending Discussions on ete

Why my script stop after the first operation

ValueError: No gradients provided for any variable (TFCamemBERT)

UTF-8 decoding when reading a MySQL column of type JSON (vs. TEXT), using Perl DBI + DBD::mysql

Symfony HttpClient Stream and chunk->getContent() Body size limit exceeded

How can I have the same size both side using ?

Python how to process complex nested dictionaries efficiently

Python Django function got multiple values for argument

Why my var return incompatibility problem with error 13?

React build looks different than React dev

In Google Sheets remove serie of ngrams from cells containing lists of comma separated ngrams in primary sheet

QUESTION

Why my script stop after the first operation

Asked 2022-Mar-11 at 12:56

I have to complete this script for a beginner BASH class but it seems like without the first line, my script fully execute its task but when I added the http / https verification (FIRST LINE) it don't go through the rest of it. Could you explain to me why? When I remove the quiet option of my grep I see that it work perfectly but it won't continue to read the script until the wget.

...

ANSWER

Answered 2022-Mar-11 at 12:56

The issue is about precedence. You need to put the error message and the exit within braces. If grep fails it prints the error message, if it succeeds, it exits.

Try this instead:

Source https://stackoverflow.com/questions/71438683

QUESTION

ValueError: No gradients provided for any variable (TFCamemBERT)

Asked 2022-Feb-11 at 13:37

Currently I am working on Named Entity Recognition in the medical domain using Camembert, precisely using the model: TFCamembert.

However I have some problems with the fine-tuning of the model for my task as I am using a private dataset not available on Hugging Face.

The data is divided into text files and annotation files. The text file contains for example:

...

ANSWER

Answered 2022-Feb-11 at 11:04

Try transforming your data into the correct format, before feeding it to model.fit:

Source https://stackoverflow.com/questions/71078218

QUESTION

UTF-8 decoding when reading a MySQL column of type JSON (vs. TEXT), using Perl DBI + DBD::mysql

Asked 2022-Jan-17 at 21:37

Here is the problem, in a working unit test. I think it's either a bug in DBI + DBD::mysql, with respect to how it handles MySQL JSON columns, or a bug in my brain.

...

ANSWER

Answered 2022-Jan-16 at 00:01

So, the answer I'm seeking now is a backward-compatible workaround, i.e., a workaround that won't break if/when DBD::mysql is fixed. Double-decoding would not be good.

You could try to determine if the JSON decode bug is present by creating a test table where you insert a non-ascii character that has a known UTF-8 encoding with byte length greater than one. For example:

Source https://stackoverflow.com/questions/70724642

QUESTION

Symfony HttpClient Stream and chunk->getContent() Body size limit exceeded

Asked 2021-Dec-19 at 13:26

In my Symfony project, I created a controller and a function to retrieve the content of an APi.json from a site.

I am using HttpClient to grab the content and embed it into a new file in the project.

However when I call this function, I have an error writing the new file:

Http2StreamException> Http2StreamException> TransportException
Body size limit exceeded

this error comes from this piece of code :

...

ANSWER

Answered 2021-Nov-27 at 01:42

So the limit you are facing comes from the $bodySizeLimit property of the Request class, which has a default value from a const there.

But you can "unlock" it, as this example in the repo itself tries to explain

so basically, you might adjust your code like this:

Source https://stackoverflow.com/questions/70130860

QUESTION

How can I have the same size both side using ?

Asked 2021-Dec-04 at 01:28

Here's my problem if I don't use a after

my image goes away like this:

So I added the , and now I have this result:

I used some margin to reduce the size of the blank space, but I'd like to be close such as this result I designed:

Here's my HTML code:

...

ANSWER

Answered 2021-Dec-03 at 23:32

Here is a flexbox sample of your code and need some change, good luck.

Source https://stackoverflow.com/questions/70221521

QUESTION

Python how to process complex nested dictionaries efficiently

Asked 2021-Nov-06 at 09:10

I have a complex nested dictionary structured like this:

...

ANSWER

Answered 2021-Nov-05 at 09:13

I was able to get about 25 % faster by combining the three processes.

Source https://stackoverflow.com/questions/69849956

QUESTION

Python Django function got multiple values for argument

Asked 2021-Oct-09 at 12:16

I am trying to call a function to print a receipt using Django in an html file. The function has 1 variable print_order_receipt(number) where the number is the order number fetched from Shopify API. This is the HTML code I did:

...

ANSWER

Answered 2021-Oct-09 at 12:16

The first parameter of a function-based view is always the request, so:

Source https://stackoverflow.com/questions/69506637

QUESTION

Why my var return incompatibility problem with error 13?

Asked 2021-Sep-16 at 15:24

I'm trying to parse Json in VBA. I'm collecting data from an API that returns a json format in a string. I use JsonConverter to parse my string. Now when i want to search on it, i got an error 13 incompatibility type.

See my Java API below :

...

ANSWER

Answered 2021-Sep-16 at 15:24

Just a quick test:

I used the JSON string you gave and the value you gave for codeAffString to build a minimal reproducible example and it does not produce any errors:

Source https://stackoverflow.com/questions/69210888

QUESTION

React build looks different than React dev

Asked 2021-Sep-14 at 17:43

I just finished the dev of my react app and ran npm run build to get my production version.

Everything works but some CSS styling...

Everything just looks perfect in my dev version but for some reason it doesn't in my build version.

Here are the problems :

My popup in dev :

My popup in build :

Here's the code for my popup :

...

ANSWER

Answered 2021-Sep-14 at 17:43

I finally found the solution !

for some unknown reason, webpack was adding ";" before some class names in my minified built CSS.

I solved the problem by simply deleting these extra ";" and know everything works as expected

Source https://stackoverflow.com/questions/69085655

QUESTION

In Google Sheets remove serie of ngrams from cells containing lists of comma separated ngrams in primary sheet

Asked 2021-Sep-02 at 12:40

Have been working in Google Sheets on a general table containing approximately a thousand texts. In one column derived form the column containing the texts in their original "written" form, are ngrams (words and the like) extracted from them, and listed in alphabetic order, one list of ngrams corresponding to each text. I’ve been trying without success to derive a second column, from these lists of such ngrams, from which I want to remove instances of certain ngrams of which I have a list (a long list, hundreds of ngrams, and a list to which I could make additions later). In other words, from the text mining vocabulary, I want to remove stop words from lists of tokens.

I tried with SPLIT and REGEXREPLACE functions, or a combination of both, but with no success.

...

ANSWER

Answered 2021-Sep-02 at 12:40

I'm not sure if I understand you correctly. If you want to remove some words from some string then basically it can be done this way:

Source https://stackoverflow.com/questions/69013437

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

Vulnerabilities

No vulnerabilities reported

Install ete

You can install using 'pip install ete' or download it from GitHub, PyPI.
You can use ete 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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