GraphConstructionError: Cannot set sequence. Illegal character in string when setting BulgeGraph sequence

[dmnfarrell]

Hi

I formerly used the following code and it worked fine:

import forgi.graph.bulge_graph as cgb
seq='TTGTCAGTTAAAAAACCACCATGCGGGGAGTTCCCTGATGGCCTGGTGGTTAGGATTCGGTGCTCTCCCTGCCATGGC'
struct = '..................((((((((((((..(.(((((((((....)))))....)))).)..))))))).))))).'
bg = cgb.BulgeGraph()
bg.from_dotbracket(struct)
bg.seq = seq

However I now get this error when I try to set the sequence.

----> 7 bg.seq = seq

/usr/local/lib/python2.7/dist-packages/forgi/graph/bulge_graph.pyc in seq(self, value)
    499             yield self.seq_ids[i]
    500 
--> 501     def create_bulge_graph(self, stems, bulges):
    502         '''
    503         Find out which stems connect to which bulges

GraphConstructionError: Cannot set sequence. Illegal character in string 'TTGTCAGTTAAAAAACCACCATGCGGGGAGTTCCCTGATGGCCTGGTGGTTAGGATTCGGTGCTCTCCCTGCCATGGC'

This occurs regardless of whether the struct is provided and is the same in python 2 and 3. Is there another way to set the sequence?

[dmnfarrell]

Note that this does work in version 0.20

[Bernhard10]

I guess this is due to the use of T instead of U (we model RNA). I guess I will change this to allow T again in version 2.0

[dmnfarrell]

Ok thanks. I reverted to version 0.20 to get the previous behaviour so it's not urgent.

[joelwebb]

Running Ubuntu Bionic on Windows with ViennaRNA 2.4.11 I am running into the same issue. Does 2.4.11 also allow use of T?

[Bernhard10]

@joelwebb For questions about the Vienna RNA package (ViennaRNA 2.4.11), please ask at https://github.com/ViennaRNA/ViennaRNA But you can always try to replace the Ts with Us

As for the forgi 2.0 library, see below

[Bernhard10]

On forgi 2.0, arbitrary characters are allowed for the sequence again. Bulge Graph creation has changed, so the code by @dmnfarrell would look like this:

import forgi.graph.bulge_graph as fgb
seq=     'TTGTCAGTTAAAAAACCACCATGCGGGGAGTTCCCTGATGGCCTGGTGGTTAGGATTCGGTGCTCTCCCTGCCATGGC'
struct = '..................((((((((((((..(.(((((((((....)))))....)))).)..))))))).))))).'
bg = fgb.BulgeGraph.from_dotbracket(struct, seq)

[Bernhard10]

The Sequence class has a is_valid function that checks for 'AUCG', but this is not called by default