Giter VIP home page Giter VIP logo

genbank's Introduction

Genbank

Hackage Build Status

Haskell cabal Genbank libary contains tools, parser and datastructures for the NCBI (National Center for Biotechnology Information) Genbank format. For more information on genbank refer to:

http://www.ncbi.nlm.nih.gov/genbank/

For a sample genbank record see:

http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html

###Datastructures for Genbank format (GenbankData.hs) Contains Haskell datastructures for Genbank format and for contained features, subfeatures ###Parse Genbank format (GenbankParser.hs) Contains Haskell functions to parse Genbank format from files or internal Strings. ###Tools for processing Genbank (GenbankTools) Contains Haskell functions to extract nucleotide sequences for features

genbank's People

Contributors

eggzilla avatar peti avatar

Stargazers

Datt Goswami avatar Omer Alkhnbashi avatar  avatar  avatar Elliot Cameron avatar Mike Panciera avatar Björn Grüning avatar David Baynard avatar Michael T. Wolfinger avatar  avatar

Watchers

James Cloos avatar  avatar  avatar  avatar

genbank's Issues

Subfeatures sanity check

Hand written genbank files contain dangling subfeatures.
Check during parsing for nestedness and correct orientation of subfeatures

Parsing error, unexpected " "

For instance parsing this file

Left "data/GCF_000482265.1_EC_K12_MG1655_Broad_SNP_genomic.gbff" (line 19660, column 6):
unexpected " "
expecting "gene", "repeat_region" or "source"

Using the latest version from hackage.

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.