augur.io.strains module

augur.io.strains.read_strains(*files, comment_char='#')

Reads strain names from one or more plain text files and returns the set of distinct strains.

Strain names can be commented with full-line or inline comments. For example, the following is a valid strain names file:

# this is a comment at the top of the file
strain1  # exclude strain1 because it isn't sequenced properly
strain2
  # this is an empty line that will be ignored.

Parameters:

files (iterable of str) – one or more names of text files with one strain name per line

Returns:

strain names from the given input files

Return type:

set