Entering edit mode
4.4 years ago
andreammo97
•
0
Hi there!
I am trying to use the function of HiddenMarkovModel that is in the module Bio.HMM.MarkovModel in Biopython. The problem is that when I run it, the output that appears on my screen is something I don't know what it is. Here it is:
HiddenMarkovModel(pr_dic, T_dic, E, T_dic, E)
Out[121]: <Bio.HMM.MarkovModel.HiddenMarkovModel at 0x7f622c13c160>
How can I get my sequence out of <Bio.HMM.MarkovModel.HiddenMarkovModel at 0x7f622c13c160>?
Thank you so much!
It's an object. You need to use one of the methods it contains to extract information from it.
Take a look at the biopython documentation for the class: https://biopython.org/docs/1.74/api/Bio.HMM.MarkovModel.html
At a glance it looks like it doesn't have a sequence emission, but has state emission functions, so you may need to use another class to actually emit the sequence from the HMM. I haven't used this bit of BioPython myself, so I don't know for sure.
Thank you so much!! I have read before that Biopython entry but I don't understand the information is displayed...
EDIT: Oh! I discovered how it works!! Thank you!!