Hi, bioBakery team~
Thanks for developing such good tools.
Recently, I am trying to use strain_transmission.py -h to find the strain transmission between two samples. However, I have no idea about what is the suggested metadata form for this script.
I have tried the similar metadata form as “add_metadata_tree.py”, but it seems didn’t work. Any suggestions are much appreciated!
Thanks!
Celine
Hi @celine77
Thanks for getting in touch. The metadata file to use the strain_transmission script has to be defined in this way:
sample_id subject_id relation_id timepoint
The sample_id has to be identical to that in the tree
The subject_id is used to define which samples correspond to the same individual. Fill with the same string as sample_id in case you don’t have longitudinal sampling.
The relation_id defines a relation between 2 or more individuals. If the sample_id is unrelated to any other sample, it should be filled with the same string as in sample_id.
The timepoint for longitudinal sampling. Fill it with 0 if you don’t have longitudinal sampling.
Only samples sharing the same relation_id will be reported by the script.
As an example:
sample_id subject_id relation_id timepoint
sample_1 subject_1 relation_1 1
sample_2 subject_2 relation_1 1
sample_3 subject_1 relation_1 2
sample_4 subject_3 relation_2 1