| ##GENERAL TEXT OR FILE MANIPULATION | |
| #Find lines in a list (e.g. file names) that are not present in another list | |
| #This is good for checking whether downstream files are present (i.e. pipeline ran susscessfully) | |
| comm -23 <(sort All.txt) <(sort Finished.txt) | |
| #Looping over anything | |
| for f in $(cat names.txt); do whatever to ${f}; done | |
| #renaming file extensions using bash code |
An example script to convert an Auspice tree JSON to a data frame for processing by downstream analyses.
This script addresses a use case of how to parse values from Augur's node data JSON files into a data frame format that can be easily consumed by other tools.
The following example shows how to convert a discrete trait analysis output from augur traits in the Nextstrain ncov workflow to a TSV file.
python3 node_data_to_table.py \
--tree results/europe/tree.nwk \
--jsons results/europe/traits.json \
| stat_smooth_func <- function(mapping = NULL, data = NULL, | |
| geom = "smooth", position = "identity", | |
| ..., | |
| method = "auto", | |
| formula = y ~ x, | |
| se = TRUE, | |
| n = 80, | |
| span = 0.75, | |
| fullrange = FALSE, | |
| level = 0.95, |