This DRAFT PR intends to provide a very simple way to find and replace taxonomy strings. For example, a user may like to fix the Escherichia-Shigella garbage, by providing the following information below as a metadata file:
id
replacements
g__Salmonella
g__Escherichia-Shigella
g__Escherichia;
g__Escherichia-Shigella;
g__Shigella
g__Escherichia-Shigella
Note: although the current implementation uses re, it does so with re.escape. So, only literal find and replace is carried out. Just keeping it simple for now.
Must do:
[x] test code
Should eventually do:
[x] add option to provide a list of pairs on the command line?
This DRAFT PR intends to provide a very simple way to find and replace taxonomy strings. For example, a user may like to fix the
Escherichia-Shigellagarbage, by providing the following information below as a metadata file:Note: although the current implementation usesre, it does so withre.escape. So, only literal find and replace is carried out. Just keeping it simple for now.Must do:
Should eventually do:
Other thoughts?