Module: IO RNA Structure

Project goals

This project aims to implement I/O routines for

• fixed interactions with pseudoknot support
• base pair probability matrix (only read)
• alignments with consensus structure

User scenario 1:

StructureFile sf ("file.db");
for (auto && rec : sf)
{
    structured_rna<rna4, dot_bracket3> structured_sequence = get<STRSEQ>(rec);
    cout << get<ENERGY>(rec) << endl;
}

User scenario 2:

StructureFile sf ("bpp.ps");
for (auto && rec : sf)
    vector<vector<double>> matrix = get<BPP>(rec);

Design ideas

A tuple of all required data is returned and can be queried through different data types.

Work packages

• Which data fields do we need? (see rna_record in SeqAn2)
• Implement the tuple to be returned. Its length is the number of data fields.
• Write constructor: support Dot_bracket, Stockholm and ViennaRNA ps format as a start (we also need fasta, but this is sequence I/O).

Files to be created

• seqan3/io/structure/ (directory)
• structure_file.hpp
• dot_bracket3.hpp
• bpp_matrix.hpp
• stockholm.hpp