funannotate | Eukaryotic Genome Annotation Pipeline | Genomics library

by nextgenusfs Python Version: 1.8.17 License: BSD-2-Clause

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

kandi X-RAY | funannotate Summary

funannotate is a Python library typically used in Artificial Intelligence, Genomics applications. funannotate 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 funannotate' or download it from GitHub, PyPI.

funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Installation, usage, and more information can be found at

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Quality

Security

License

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Support

funannotate has a low active ecosystem.

It has 245 star(s) with 78 fork(s). There are 15 watchers for this library.

There were 1 major release(s) in the last 12 months.

There are 172 open issues and 692 have been closed. On average issues are closed in 43 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of funannotate is 1.8.17

Quality

funannotate has 0 bugs and 0 code smells.

Security

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

funannotate code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

funannotate is licensed under the BSD-2-Clause License. This license is Permissive.

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

Reuse

funannotate 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 are not available. Examples and code snippets are available.

funannotate saves you 11249 person hours of effort in developing the same functionality from scratch.

It has 27532 lines of code, 782 functions and 55 files.

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

Top functions reviewed by kandi - BETA

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

This function creates EVM partitions
Find the index of the left start of a given interval
Returns an iterator over the elements in the given range
Find the ranges in the input file
Summarize the annotation
Execute a command
Convert FUNDB databases to JSON
Return the version of the program
Parse command line arguments
Parse egg mapper output
Get annotation for GK annotation
Combine multiple GTM models into a single GTF file
Convert BAM files to ExonsHints
Convert GO IDDict to table
Concatenate annotation table
Map nucleotide sequences
Parse antismash results
Define the parameters for analysis
Retrieve training models for training training
Run PASA
Compares two annotated annotations
Create annotation table
Convert a dict to GFF3 format
Convert GbK to PASTA format
Convert a GFF file to pasa
Compares two GTK files and returns a dictionary of dicts for each reference

Get all kandi verified functions for this library.

funannotate Key Features

No Key Features are available at this moment for funannotate.

funannotate Examples and Code Snippets

No Code Snippets are available at this moment for funannotate.

Community Discussions

Trending Discussions on funannotate

QUESTION

Asked 2021-Oct-30 at 09:03

I use a docker container in the following way:

...

ANSWER

Answered 2021-Oct-30 at 09:03

If the container keeps running you can use docker exec -ti bash (or sh) to execute a shell inside your container with an interactive terminal.

Maybe you can also add a shell or command with docker run [OPTIONS] IMAGE[:TAG] [COMMAND] [ARG...]

This worked for me

Source https://stackoverflow.com/questions/69778085

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

Vulnerabilities

No vulnerabilities reported

Install funannotate

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