get_raw_coverage_table attribute

[elizabethmcd]

When trying to run the .get_raw_coverage_table attribute from the documentation, I get the following error:

Type "help", "copyright", "credits" or "license" for more information.
>>> import inStrain
>>> import inStrain.SNVprofile
>>> IS=inStrain.SNVprofile.SNVprofile("results/CAPIIB.IS/")
>>> coverage_table = IS.get_raw_coverage_table()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: 'SNVprofile' object has no attribute 'get_raw_coverage_table'

I looked in the SNVprofile.py script and couldn't find that attribute defined. The .get_nonredundant_scaffold_table method worked when I tried that.

[MrOlm]

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Hope that helps and sorry for the out-of-date docs!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