Comments (1)
Hello,
I just looked into that and you are indeed correct, this method seems to have been deprecated several inStrain versions ago. I will add back this method in a more sensical way soon.
In the meantime you can access the raw coverage values by running IS.get('covT')
. This will return a covT
object, which is a goofy object that consists of a series of nested dictionaries. I can go into detail if you'd like, but if you'd just like an array of coverage values, you can run cov = inStrain.profile.profile_utilities.mm_counts_to_counts_shrunk(covT[scaff])
on your covT object, where scaff
is the name of the scaffold you'd like the coverage for. This will return a pandas Series object where the index is the position on the scaffold (0-based), and the value is the coverage at that base. Positions with no coverage will not be in this object.
Hope that helps and sorry for the out-of-date docs!
-Matt
from instrain.
Related Issues (20)
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