Git Product home page Git Product logo

deepbgc's Introduction

DeepBGC: Biosynthetic Gene Cluster detection and classification.

Install DeepBGC

  • Run pip install deepbgc to install the deepbgc python module.

Prerequisities

  • Install Python 3.6 (version 3.7 is not supported by TensorFlow yet)
  • Install Prodigal and put the prodigal binary it on your PATH: https://github.com/hyattpd/Prodigal/releases
  • Install HMMER and put the hmmscan and hmmpress binaries on your PATH: http://hmmer.org/download.html
  • Download and extract Pfam database from: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/Pfam-A.hmm.gz

Use DeepBGC

Detection

Detect BGCs in a genomic sequence.

# Show detection help
deepbgc detect --help

# Detect BGCs in a nucleotide sequence
deepbgc detect --model DeepBGCDetector_v0.0.1.pkl --pfam Pfam-A.hmm --output myCandidates/ myInputSequence.fa

# Detect BGCs with >0.9 score in existing Pfam CSV sequence
deepbgc detect --model myModel.pkl --output myStrictCandidates/ -s 0.9 myCandidates/myCandidates.pfam.csv

Classification

Classify BGCs into one or more classes.

# Show classification help
deepbgc classify --help

# Predict biosynthetic class of detected BGCs
deepbgc classify --model RandomForestMIBiGClasses_v0.0.1.pkl --output myCandidates/myCandidates.classes.csv myCandidates/myCandidates.candidates.csv

deepbgc's People

Contributors

jasonmvictor avatar

Watchers

avatar

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.