ncbi-genome-download | Scripts to download genomes from the NCBI FTP servers | Genomics library

by kblin Python Version: 0.3.3 License: Apache-2.0

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

kandi X-RAY | ncbi-genome-download Summary

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

Some script to download bacterial and fungal genomes from NCBI after they restructured their FTP a while ago. Idea shamelessly stolen from Mick Watson's Kraken downloader scripts that can also be found in Mick's GitHub repo. However, Mick's scripts are ~~written in Perl~~ specific to actually building a Kraken database (as advertised). So this is a set of scripts that focuses on the actual genome downloading.

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Security

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Support

ncbi-genome-download has a low active ecosystem.

It has 759 star(s) with 163 fork(s). There are 31 watchers for this library.

There were 2 major release(s) in the last 12 months.

There are 37 open issues and 89 have been closed. On average issues are closed in 452 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of ncbi-genome-download is 0.3.3

Quality

ncbi-genome-download has 0 bugs and 0 code smells.

Security

ncbi-genome-download has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

ncbi-genome-download code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ncbi-genome-download 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

ncbi-genome-download 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, examples and code snippets are available.

It has 2097 lines of code, 181 functions and 16 files.

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

Top functions reviewed by kandi - BETA

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

Argument parser
Return the available choices for a category
Return the default value for a given category
Return argparse argument parser
Download files
Run download
Create download jobs for the given entry
Create a Config from keyword arguments
Run Ngd config download
Creates a download job
Creates a Config from a namespace
Convert taxids to taxids
Set the groups
Create a list from input
Write the descendent taxa for a taxid
Validate file formats
Write taxon information
Validate type_materials
Set the assembly levels
Set the refseq_categories
Try to read the version of the NCBI

Get all kandi verified functions for this library.

ncbi-genome-download Key Features

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ncbi-genome-download Examples and Code Snippets

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Community Discussions

Trending Discussions on ncbi-genome-download

Linking files downloaded in a loop, to an identifier in a text list with a bash loop

QUESTION

Linking files downloaded in a loop, to an identifier in a text list with a bash loop

Asked 2018-Jun-29 at 12:59

I have a bash loop which is using a python program to loop over each identifier in a list (text file), to download genomes (files), I'm wondering whether there is a way I can link each file download to the id in the list, as the downloaded files have names which make it more difficult to use later on.

The loop in bash:

...

ANSWER

Answered 2018-Jun-29 at 12:59

For sure there should be a way. But we need more information: which are the names of the files you are downloading?

Source https://stackoverflow.com/questions/51078528

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

Vulnerabilities

No vulnerabilities reported

Install ncbi-genome-download

Alternatively, clone this repository from GitHub, then run (in a python virtual environment).

Support

This script lets you find out what TaxIDs to pass to ngd, and will write a simple one-item-per-line file to pass in to it. It utilises the ete3 toolkit, so refer to their site to install the dependency if it's not already satisfied. You can query the database using a particular TaxID, or a scientific name. The primary function of the script is to return all the child taxa of the specified parent taxa. The script has various options for what information is written in the output.

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