Software

10. sbmlcore

Collection of core classes to help with building structure- and chemistry-based feature datasets to train machine learning models to predict antimicrobial resistance.

9. tb-predict-pipeline

NextFlow pipeline that encapsualtes gnomonicus.

8. gnomonicus

Takes

  1. a variant call file (vcf) file output from a genetics processing pipeline
  2. a resistance catalogue
  3. a reference genome, as a GenBank file

and produces

  1. a list of antibiotics and their predicted effects
  2. CSV files of the discerned mutations and genetic variants

Designed to be the basis of a TB analysis pipeline. Based on piezo and gumpy.

7. piezo

A python3 package that contains a single class, ResistanceCatalogue that is instantiated with a resistance catalogue described using the GARC grammar. The instance has a predict method that returns a dictionary containing the appropriate predictions for the antibiotics.

A number of published tuberculosis resistance catalogues described using the GARC grammar can be found here.

6. gumpy

This is a contraction of “Genetics with Numpy”. It is a series of classes, based primarily on a Genome object that is instantiated by a GenBank file. Gumpy is pythonic with appropriately overloaded operators; for example subtracting one genome from another yields a GenomeDifference object.

5. bashthebug

This is built off pyniverse, this adds some analysis specific to this project.

4. pyniverse

This is a generic Python package able to analyse the downloaded classifications from a Zooniverse project. It automatically produces a series of graphs describing (i) how many classifications have been made every day/week/month as well as (ii) how many new users have signed up and (iii) the resulting Gini curve.

Example graph produced by pyniverse showing number of classifications done per week by the volunteers of a Zooniverse project

3. AMyGDA

For a more detailed description of my Automated Mycobacterial Growth Detection Algorithm, including how to download, please go to the AMyGDA page.

2. pygsi

A python3 package that provides a simple class, NucleotideStretch, for systematically and programmatically determining how many minor variations of a specified sequence of nucleotides exist in the Sequence Read Archive using the BIGSI index. As an example, some Python is included that counts how many variants of OXA-1 have been deposited in the SRA.

1. jitter

I like jitter plots, but neither of my standard plotting tools, gnuplot and matplotlib, were equipped to do them, so I wrote this simple Python to ‘jitter’ some data.