Datasets for testing McCoy

This repo contains data and scripts for testing the realtime phylodynamics package McCoy.

process data into groups

McCoy works with data collected overtime. To convert the datasets into time period grouped fasta files use the group.py script.

python group.py data/Ebola/Full-EbolaTest-2015-42.fasta --period month

Use the --date-format, --delimiter, and --location to process other date formats.

python group.py data/Influenza/InfluenzaAH3N2_HAgene_2009_California.fasta --date-format "%Y/%m/%d" --delimiter "_" --location -1 

Use --date-format decimal to parse decimal dates.

python group.py data/SARS-CoV-2/SARS-CoV-2-VIC.fasta --date-format decimal

Use --cumulative to create a cumulative dataset.

python group.py data/Ebola/Full-EbolaTest-2015-42.fasta --period month --cumulative

--help

usage: group.py [-h] [--period {day,week,month}] [--date-format DATE_FORMAT] [--delimiter DELIMITER] [--location LOCATION] [--cumulative] FASTA

Group Fasta by time period.

positional arguments:
  FASTA

optional arguments:
  -h, --help            show this help message and exit
  --period {day,week,month}
  --date-format DATE_FORMAT
  --delimiter DELIMITER
  --location LOCATION
  --cumulative