Biobase- Base library for bioinformatics



Turner file parser. Returns a Turner2004 data structure. We store data in the same way it is stored in the ViennaRNA package. Pairs are tuples however.

How is stack data stored:

AX UY -> ((A,U),(Y,X))

How iloop1x1 is stored:

X A G U C -> ((A,U),(C,G),X,Y) Y

Now iloop1x2 is stored:

X A G U C -> ((A,U),(C,G),X,C,Y), single (X) first, then 5' to 3' YC

iloop2x2 is stored:

XY A G U C -> ((A,U),(C,G),X,Y,y,x), X-->Y then x<--y xy

TODO not sure if dangle3/dangle5 are correctly split or if they should switch