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gecrooks / weblogo

WebLogo 3: Sequence Logos redrawn
weblogo.threeplusone.com
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How can i make new alphabet? #73

Closed MarcGrad closed 6 years ago

MarcGrad commented 6 years ago

I need selenocysteine in logo. But reduced_protein_alphabet don't work. I dont understand docstring about weblogolib.Alphabet.new(). 

weblogolib.Alphabet.__new__('ACDEFGHIKLMNPQRSTVUWY', zip('acdefghiklmnpqrstvuwy','ACDEFGHIKLMNPQRSTVUWY'))
Traceback (most recent call last):

  File "<ipython-input-114-1c1286ba9c1d>", line 1, in <module>
    weblogolib.Alphabet.__new__('ACDEFGHIKLMNPQRSTVUWY', zip('acdefghiklmnpqrstvuwy','ACDEFGHIKLMNPQRSTVUWY'))

  File "/home/marcin/.conda/envs/my_root/lib/python3.6/site-packages/corebio/seq.py", line 185, in __new__
    self = object.__new__(cls)

TypeError: object.__new__(X): X is not a type object (str)
gecrooks commented 6 years ago

You don't need to call new() directly. Just instantiate a class as usual.

weblogolib.Alphabet('ACDEFGHIKLMNPQRSTVUWY', zip('acdefghiklmnpqrstvuwy','ACDEFGHIKLMNPQRSTVUWY'))