Introduction¶

forgi is a library for manipulating RNA as a graph-like structure. It provides classes for reading, storing, manipulating and outputting RNA structures. It classifies and stores RNA secondary structure in a data structure that quickly allows one to determine which structural elements are connected and which nucleotides they contain.

However, some taske ar ebetter performed on the dotbracket structure or the pair-table representation of an RNA. For this, the forgi.utilities module provides useful functions.

Dot-bracket to pair-table¶

Converting a secondary structure in dot-bracket format to a pairtable:

>>> import forgi.utilities.stuff as fus
>>> fus.dotbracket_to_pairtable('((..))..((..))')
[14, 6, 5, 0, 0, 2, 1, 0, 0, 14, 13, 0, 0, 10, 9]

The pair-table list has the number of nucleotides as the first element. Every subsequent entry at position i contains the pairing partner of the i’th nucleotide. If the value at position i is 0, then nucleotide i is unpaired.

Pair-table to dot-bracket¶

Converting a pair-table to a dot-bracket representation:

>>> import forgi.utilities.stuff as fus
>>> fus.pairtable_to_dotbracket([14, 6, 5, 0, 0, 2, 1, 0, 0, 14, 13, 0, 0, 10, 9])
'((..))..((..))'