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Junctions generate not only regular multiloops but also other structures #51

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Rimasss opened this issue Apr 24, 2023 · 0 comments
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@Rimasss
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Rimasss commented Apr 24, 2023

According to the documentation junctions returns A list of tuples of multiloop segments. Each tuple contains the segments of one regular (i.e. not pseudoknotted) multiloop.
but the output isn't always a list of only regular multiloops, for example:

>>> dbn= '...(((((((..((((((.........))))))......).((((((.......))))))..))))))...'
>>> bg, = forgi.load_rna(dbn)
>>> bg.junctions
[('f0', 't0'), ('m0', 'm1', 'm2')]

Although the output list is intended to indicate the quantity of regular multiloops, which is two in this instance, an inspection of the graph produced by Forna reveals that there is only one regular multiloop.

image

In addition, using describe_multiloop(multiloop)[source] we get:

>>> bg.describe_multiloop(('f0', 't0'))
{'open'}
>>> bg.describe_multiloop(('m0', 'm1', 'm2'))
{'regular_multiloop'}
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