Handle pre-calculated structures

[dgruano]

This PR implements key changes to externalize calculation of secondary structures by RNAfold. More specifically:

• Add secondary_structure argument indicating that the input sequences contain secondary structures.
• Add utility function to parse secondary structure files. These must be FASTA files where the sequence is a concatenation of the nucleotide sequence, the SS in dot bracket notation and optionally the minimum free energy (MFE).
• Add logic to handle SS data and skip RNAfold execution.
• Filter out SS data that corresponds to otherwise filtered sequences (i.e., sequences with unsupported characters or sequences outside the 200 to 20000 nt range.