https://github.com/hernanmd/covid-2019
Analysis of Coronavirus outbreak data with Pharo
https://github.com/hernanmd/covid-2019
analysis bioinformatics coronavirus coronavirus-analysis coronavirus-tracking covid-19 covid-virus ncov-2019 pharo smalltalk
Last synced: 5 months ago
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Analysis of Coronavirus outbreak data with Pharo
- Host: GitHub
- URL: https://github.com/hernanmd/covid-2019
- Owner: hernanmd
- Created: 2020-01-31T07:49:11.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2023-08-16T14:50:16.000Z (about 2 years ago)
- Last Synced: 2025-04-19T21:25:35.984Z (6 months ago)
- Topics: analysis, bioinformatics, coronavirus, coronavirus-analysis, coronavirus-tracking, covid-19, covid-virus, ncov-2019, pharo, smalltalk
- Language: Smalltalk
- Homepage:
- Size: 44.9 KB
- Stars: 7
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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# Introduction
Analysis of Coronavirus outbreak data with [Pharo](https://www.pharo.org) 8.x
# Installation
```smalltalk
Metacello new
baseline: 'COVID19';
repository: 'github://hernanmd/COVID-2019/src';
load.
```
# Usage
## Data Visualization
For visualization of cases as provided by CSSEGISandData, evaluate in Pharo 8:
```smalltalk
BioCOVID19Viz exampleLiveData
```
## Alignment
For genomic analysis install [BioSmalltalk](https://github.com/hernanmd/BioSmalltalk) and evaluate the following one-liner to align the sequences with MAFFT:
```smalltalk
BioCOVID19GenomicAnalysis alignSeqs.
```
To add accession numbers as they appear in the NCBI GenBank repository, edit the class side methods matching the sequencing location:
- seqsFromChina
- seqsFromItaly
- seqsFromUSA
- ...
The resulting alignment is written in 'mafft_output.align' in the Pharo image directory.
Accessions are retrieved from https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Wuhan%20seafood%20market%20pneumonia%20virus,%20taxid:2697049
## Reference Genome download
To download the latest build of the reference genome (as of 01/02/2020) from NCBI:
```smalltalk
BionCoV2019GD new download.
```
Downloaded files are located into the Pharo image directory.
# Misc
To create a GitHub Pharo project with Continuous Integration support from scrath follow [this video](https://www.youtube.com/watch?v=Wnt3OBhR18I).
# ToDo
- Download accessions from here: https://dev.ncbi.nlm.nih.gov/core/assets/genbank/files/ncov-sequences.yaml (currently restricted access?)
- Add sequences from GISAID
- Evaluate MAFFT alignment quality.
# Sample output
