mirador/ebola-data

Demographic, clinical, and SNP data for the first EBOV patients in the Sierra Leone ## Creating Ebola dataset for Mirador 1) Requirements: - PyVCF package: pyvcf.readthedocs.org 2) Convert the MasterDataListandEBOVResults, DemographicsFromSim, CaseNotification, and FinalPiccoloData Excel spreadsheets into csv format using csvkit: ```bash in2csv sources/xls/MasterDataListandEBOVResults.xlsx --sheet Ebola_js1 > sources/csv/MasterDataListandEBOVResults.csv in2csv sources/xls/DemographicsFromSim_schieffelin.xlsx > sources/csv/DemographicsFromSim_schieffelin.csv in2csv sources/xls/CaseNotification_schieffelin.xlsx > sources/csv/CaseNotification_schieffelin.csv in2csv sources/xls/FinalPiccoloData_schieffelin.xlsx --sheet FinalSummary1 > sources/csv/FinalPiccoloData_schieffelin-FinalSummary1.csv ``` 3) Run the makedataset.py script that will generate the aggregated dataset in Mirador's format and will store it in the mirador folder. ```bash python makemira.py ``` The arguments -seq needs to be added in order to aggregate the sequencing data into the Mirador's dataset, and -log can be used to convert the viral loads into log units using the formula log(1 + qpcr) where qpcr is the qPCR measurement: ```bash python makemira.py -log -seq ``` ## Creating Ebola dataset as single CSV file The Mirador dataset can be converted into a single CSV file that can be more convenient for loading into other tools by running the following script: ```bash python makecsv.py -in mirador -out csv/ebola-data.csv ``` This can be done only after generating the Mirador dataset, and will generate an ebola-data.csv in the csv folder. ## Creating SPSS dataset The Mirador dataset can also be converted into an SPSS-compatible format, loadable from repositories like the Dataverse, using the makespss script: ```bash python makespss.py -in mirador -out csv/ebola-data.csv ``` , which also saves a SPSS-style control card in csv/ebola-data.spss. ## SNP, iSNV and cluster data The aggregated Mirador file includes the Single Nucleotide Polymorphism (SNP) data …