EDTA | Extensive de-novo TE Annotator | Genomics library

by oushujun Perl Version: v2.1.0 License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(4)Vulnerabilities Install Support

kandi X-RAY | EDTA Summary

EDTA is a Perl library typically used in Artificial Intelligence, Genomics applications. EDTA has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

This package is developed for automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries. The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome. For benchmarking of a testing TE library, I have provided the curated TE annotation (v6.9.5) for the rice genome (TIGR7/MSU7 version). You may use the lib-test.pl script to compare the annotation performance of your method/library to the methods we have tested (usage shown below).

Support

Quality

Security

License

Reuse

Support

EDTA has a low active ecosystem.

It has 236 star(s) with 55 fork(s). There are 7 watchers for this library.

It had no major release in the last 12 months.

There are 38 open issues and 308 have been closed. On average issues are closed in 119 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of EDTA is v2.1.0

Quality

EDTA has 0 bugs and 0 code smells.

Security

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

EDTA code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

EDTA 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

EDTA releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

It has 2249 lines of code, 111 functions and 22 files.

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

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EDTA Key Features

No Key Features are available at this moment for EDTA.

EDTA Examples and Code Snippets

No Code Snippets are available at this moment for EDTA.

Community Discussions

Trending Discussions on EDTA

Sort Option children by index value for both parent Selects (Javascript Only)

Remove all repeatable values from the list and the values that are inside other values, Python

Select multiple filters, display only markers that have common features

Passing values between activity

QUESTION

Sort Option children by index value for both parent Selects (Javascript Only)

Asked 2022-Apr-16 at 19:45

I'm trying to create a Dual List Box using only vanilla Javascript, no JQuery or JS packages, for learning purposes.

When a user double-clicks an Option, that Option appends to the other parent Select (boxB) and is removed from the original parent Select (boxA), and vice versa. The Option elements have data-index attributes with ascending numerical values. How do I maintain the numerical order of the Options by index value, regardless of which parent Select they append?

...

ANSWER

Answered 2022-Apr-16 at 19:45

Since you are basically using the same logic for both selects, I consolidated into one function. Rather than use ID's, which can be problematic, we can use a single className and rely on basic JS to determine which is which. The sorting mechanism - your original question - works by taking all the option elements into an array, sorting the array by dataset.index, and then repopulating the select element. One set of logic works for both boxes

Source https://stackoverflow.com/questions/71896654

QUESTION

Remove all repeatable values from the list and the values that are inside other values, Python

Asked 2020-Oct-26 at 18:11

My list contains of sentences. There are sentences that can be repeated and there are sentences that are inside some other sentences. For example:

'Heterocyclic compounds'
'Heterocyclic compounds having oxygen'

Number 1 is inside number 2 so I need to keep only unique one that is number 2.

Part of my list:

...

ANSWER

Answered 2020-Oct-26 at 18:04

You can make 2 nested loops on the list and for each string you compare with the other, you keep track of longest one the save the results per string. It might not be an optimal solution if you have large data

Code

Source https://stackoverflow.com/questions/64542326

QUESTION

Select multiple filters, display only markers that have common features

Asked 2020-May-05 at 08:16

I have a leaflet map, already working. Currently, I have multiple checkbox filters (almost 40 in total on two maps) : a user can select several markers at the same time. The filters represent "specialities", and when I click on a filter ,it show me the hospitals that have that speciality. So on the map, I can have clusters that show a hospital with several specialities, and individual markers that show differents hospitals with one speciality.

If a user clicks on the filter A, it display for example 5 markers with feature A.
If a user clicks on the filter B, it displays 5 markers with feature B.
And when a user clicks on filters A & B together, it displays A + B, so the 10 markers, with individual markers, and clustered markers.

What I'm trying to do:

Each individual chekcbox must show corresponding markers, BUT as soon as I check several checkboxes at the same time, I want to display only the markers (hospital) where I can find the corresponding features. For example, if I click on filter A and B together, I would like to see only the hospitals where there are speciality A and B and hide marker with only one feature.

As I already coded all my functions, I want to avoid rebuilding new GeoJSON features. I tried but it duplicate the markers.

I'm looking for a loop like this (of course this is not working):

...

ANSWER

Answered 2020-May-04 at 22:38

Let's assume a simplified version of your dataset, e.g. a GeoJSON FeatureCollection containing points for clinics/departments in hospitals, where two (or more) clinics pertaining to the same hospital share the same position:

Source https://stackoverflow.com/questions/61535917

QUESTION

Passing values between activity

Asked 2020-Jan-13 at 21:34

I should show 2 TextView in MainActivity "stringadaA" and "numerodaB" , namely the string and the number put in the 2 activities A and B.These values must not be lost in the transition between the activities but must change only when they are changed by the user. I managed to do it but when I press the "Ritorna" button to go back to the MainActivity it does not maintain both the results as I would expect, why are not both saved if I insert values in ActivityA and ActivityB?

Thanks in advance

...

ANSWER

Answered 2020-Jan-12 at 21:18

Use startActivityForResult method to invoke ActivityA and ActivityB. And override onActivityResult method in your MainActivity.

Here, 100 is a int value request code for ActivityA :

Source https://stackoverflow.com/questions/59707434

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

Vulnerabilities

No vulnerabilities reported

Install EDTA

There are many ways to install EDTA. You just need to find the one that is working for your system. If you are not using macOs, you may try the conda appraoch before the Singularity apprapch.
Download the latest EDTA:.
Visit dockerhub for a list of available tags (e.g., 1.9.5). Where {path} is the path you build the EDTA singularity image.
Visit dockerhub for a list of available tags (e.g., 1.9.5).
singularity pull EDTA.sif docker://quay.io/biocontainers/edta:1.9.5
docker pull quay.io/biocontainers/edta:1.9.5
Compile using your local docker with the Dockerfile in this package:
It is tricky (for me) to specify files with a path to run EDTA. Softlinked files are considered "with path". So please copy all the files to your work directory to run Singularity/docker containers of EDTA.
Similarily, it is tricky to specify paths to dependency programs (i.e., repeatmasker, repeatmodeler).

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: