Posts

A phylogenetic tree viewer with Qt and Toytree

26 February 2021

Toytree is a Python library for tree manipulation and plotting. So it can be used to view phylogenetic trees. The goal of Toytree is to provide a light-weight Python equivalent to commonly used tree manipulation and plotting libraries in R. It’s based on toyplot which uses Javascript and html, making plots self-contained and embeddable in browsers. Implementation

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A simple GIS plugin for Tablexplore

16 February 2021

Tablexplore is an application for data analysis and plotting built in Python using the PySide2/Qt toolkit. The interface allows quick visualization of data with convenient plotting. The program is intended mainly for educational/scientific use but should be useful for a variety of general applications. The program also has a plugin system that allows extra functionality to be added arbitrarily. These could be run in separate windows or placed in a pane inside the main application, under the table. From the...

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Ireland deaths in 2019/2020 compared to previous years

28 January 2021

In a previous post we looked at Ireland daily deaths data from 2019/2020 from RIP.ie. Here we can compare those two recent years to monthly data from the CSO for the years 2005-2018. This data is found here. Here we use CSO monthly figures up to 2018 and combine them with the data taken from the RIP.ie website for 2019 and 2020. The Jupyter notebook with this code is available here. The data files referred to in the code are...

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Daily deaths in Ireland from RIP.ie in 2019 and 2020

25 January 2021

Deaths in Ireland must be registered by law and are held in the General Register Office (GRO) which is the central civil repository for records relating to Births, Marriages and Deaths. A death can be registered with any Registrar, irrespective of where it occurs. Deaths must be registered as soon as possible after the death and no later than three months. So there is a delay of a few months before death figures can be considered completely accurate. In any...

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Visualizing Irish girls names since 1970

20 January 2021

The CSO (Central Statistics Office of Ireland) publishes a list of the baby names registered every year with number of births for each. The data goes back to 1967. So we can see which names are most popular every year and how they change over time. This post uses Python, seaborn and matplotlib to visualise the data in various ways. The code for making these plots can be shown underneath each one or the complete code viewed in the Jupyter...

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M. bovis spoligotyping from WGS reads

15 January 2021

Spoligotyping (spacer oligonucleotide typing) is a widely used genotyping method for M. tb (Mycobacterium tuberculosis species), which exploits the genetic diversity in the direct repeat (DR) locus in Mtb genome. Each DR region consists of several copies of the 36 bp DR sequence, which are interspersed with 34 bp to 41 bp non-repetitive spacers. A set of 43 unique spacer sequences is used to classify Mtb strains based on their presence or absence. This a molecular method traditionally conducted using...

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Linux application packaging and universal formats

11 January 2021

Linux is an amazing open source operating system used universally across industry, in science, on embedded hardware and on servers. The core system and kernel are typically packaged up into ‘distributions’ for end users. So we have Ubuntu, Fedora, Debian and endless others. These are really variants on the same thing but some are specialised for desktop or server use (or something more specific like security). Actually there are far too many distributions but only a few are widely used....

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Detecting polymorphisms in the RD900 region of MTBC species

23 December 2020

We have just published a paper detailing variation across the Mycobacterium tuberculosis Complex (MTBC) in the RD900 region. This region was first described as a lineage specific locus in M. africanum GM041182 strain (Bentley et al. 2012) and was thought to be deleted in M. bovis and “modern” M. tuberculosis lineages. RD900 region was not present in the original M. bovis AF2122/97 reference genome annotation, but was found to be actually present upon resequencing. These species show more than 99%...

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Tablexplore - a desktop tool for table analysis

19 December 2020

Tablexplore is an application for data analysis and plotting built in Python using the PySide2/Qt toolkit. The interface allows quick visualization of data with convenient plotting. The primary goal is to let users explore their tables interactively without any prior programming knowledge and make interesting plots as they do this. The program is intended mainly for educational/scientific use but should be useful for a variety of general applications. This isn’t a replacement for a spreadsheet as such. Instead it’s meant...

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Epidemics, PCR and the dangers of mass testing

29 November 2020

The American Society for Microbiology (ASM) has just published a discussion article concerning the use of mass testing for SARS-CoV-2 and it’s possible implications. The concerns raised have serious implications for future testing practice. Very early on when the SARS-CoV-2 virus was detected in China, PCR tests were developed for detecting the presence of viral RNA in sputum samples. This is the so-called swab test. PCR stands for Polymerase chain reaction. The method used in this case is RT-PCR becuase...

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