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bionode-fasta's Introduction

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bionode.io

bionode

Modular and universal bioinformatics

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Install

You need to install the latest Node.JS first, please check nodejs.org or do the following:

# Ubuntu
sudo apt-get install npm
# Mac
brew install node
# Both
npm install -g n
n stable

To use bionode as a command line tool, you can install it globally with -g.

npm install bionode -g

Or, if you want to use it as a JavaScript library, you need to install it in your local project folder inside the node_modules directory by doing the same command without -g.

npm i bionode # 'i' can be used as shorcut to 'install'

Documentation

Check our documentation at doc.bionode.io

Modules list

For a complete list of bionode modules, please check the repositories with the "tool" tag

Contributing

We welcome all kinds of contributions at all levels of experience, please read the CONTRIBUTING.md to get started!

Communication channels

Don't be shy! Come talk to us ๐Ÿ˜ƒ

Who's using Bionode?

For a list of some projects or institutions that we know of, check the USERS.md file. If you think you should be on that list or know who should, let us know! :D

Acknowledgements

We would like to thank all the people and institutions listed below!

bionode-fasta's People

Contributors

alanrice avatar ayangromano avatar bmpvieira avatar cmdcolin avatar erictleung avatar katrinleinweber avatar rudani avatar

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bionode-fasta's Issues

Remove zlib dependency, replace with core Node api

Just reading through, checking dependency readmes, and turns out zlib (which does not come up with search on npm), is now deprecated as mentioned here. Functionality has been folded into Node core.

This brings up another topic: how to migrate to new Node versions? I think a lot of bionode is from the "v0.12 era"? I've been using the LTS Node 4 for web projects currently. But the new versions bring in some really sweet ES6 features, and I think bionode is less susceptible to "complex environments that find it cumbersome to continually upgrade" [1] and so should be OK to use the latest stable release. But I guess also, should try to stick to LTS as long as the stable features aren't super worth it. I heard that they are trying to match up v6 with V8 5.x or so for something like 95% ES6 support, so thats something nice to look out for.

Determine if sequence type is necessary

Having the sequence type determined in the output is useful for converting to other formats that require it, but maybe they should have the dependancy and not bionode-fasta?

If sequence type isn't necessary then bionode dependency isn't needed and webpack can be a lot smaller.

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