The Vienna format (dot bracket notation) for RNA sequences with secondary structure.
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template<typename stream_type , typename seq_legal_alph_type , bool structured_seq_combined, typename seq_type , typename id_type , typename bpp_type , typename structure_type , typename energy_type , typename react_type , typename comment_type , typename offset_type > |
void | read_structure_record (stream_type &stream, structure_file_input_options< seq_legal_alph_type, structured_seq_combined > const &options, seq_type &seq, id_type &id, bpp_type &bpp, structure_type &structure, energy_type &energy, react_type &react, react_type &react_err, comment_type &comment, offset_type &offset) |
| Read from the specified stream and back-insert into the given field buffers. More...
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template<typename stream_type , typename seq_type , typename id_type , typename bpp_type , typename structure_type , typename energy_type , typename react_type , typename comment_type , typename offset_type > |
void | write_structure_record (stream_type &stream, structure_file_output_options const &options, seq_type &&seq, id_type &&id, bpp_type &&bpp, structure_type &&structure, energy_type &&energy, react_type &&react, react_type &&react_err, comment_type &&comment, offset_type &&offset) |
| Write the given fields to the specified stream. More...
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void | read_structure_record (stream_type &stream, structure_file_input_options< seq_legal_alph_type, structured_seq_combined > const &options, seq_type &seq, id_type &id, bpp_type &bpp, structure_type &structure, energy_type &energy, react_type &react, react_type &react_err, comment_type &comment, offset_type &offset) |
| Read from the specified stream and back-insert into the given field buffers. More...
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static inline std::vector< std::string > | file_extensions |
| The format type is required to provide a vector of all supported file extensions.
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void | write_structure_record (stream_type &stream, structure_file_output_options const &options, seq_type &&seq, id_type &&id, bpp_type &&bpp, structure_type &&structure, energy_type &&energy, react_type &&react, react_type &&react_err, comment_type &&comment, offset_type &&offset) |
| Write the given fields to the specified stream. More...
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static inline std::vector< std::string > | file_extensions |
| The format type is required to provide a vector of all supported file extensions.
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The Vienna format (dot bracket notation) for RNA sequences with secondary structure.
Introduction
Dot Bracket or Vienna Notation is widely used for secondary structure annotation. Is is a very simple format, containing one or more sequences. Each sequence must appear as a single line in the file. A sequence may be preceded by a special line starting with the '>' character followed by a sequence name (like FastA). After each sequence line there is usually a line containing secondary structure, using brackets to denote interacting nucleotides or amino acids, and dots for unpaired sites. The length of the struture must equal the length of the sequence. Optionally, the structure may be followed by a space character and the minimum free energy value enclosed in parentheses (). Note that there cannot be energy without structure.
The Vienna format is the output format of RNAfold. Furthermore, it is designed to be compatible with the input format of the ViennaRNA package (if structure and energy are omitted). See https://www.tbi.univie.ac.at/RNA/tutorial/#sec2_7 for details.
fields_specialisation
The Vienna format provides the fields seqan3::field::seq, seqan3::field::id, seqan3::field::bpp (read only), seqan3::field::structure, seqan3::field::structured_seq and seqan3::field::energy.
If you select seqan3::field::structured_seq you must not select seqan3::field::seq or seqan3::field::structure.
Either the field seqan3::field::seq or the field seqan3::field::structured_seq is required when writing.
The field seqan3::field::bpp is ignored when writing, but a structure string can be converted to bpp when reading.
Implementation notes
When reading the ID-line the identifier (>
) and any blank characters before the actual ID are stripped. Each field is read/written as a single line (except ENERGY, which goes right after the structure). Numbers and spaces within the sequence are simply ignored, but not within the structure.
template<typename stream_type , typename seq_legal_alph_type , bool structured_seq_combined, typename seq_type , typename id_type , typename bpp_type , typename structure_type , typename energy_type , typename react_type , typename comment_type , typename offset_type >
void seqan3::format_vienna::read_structure_record |
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stream_type & |
stream, |
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structure_file_input_options< seq_legal_alph_type, structured_seq_combined > const & |
options, |
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seq_type & |
seq, |
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id_type & |
id, |
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bpp_type & |
bpp, |
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structure_type & |
structure, |
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energy_type & |
energy, |
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react_type & |
react, |
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react_type & |
react_err, |
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comment_type & |
comment, |
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offset_type & |
offset |
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inlineprotected |
Read from the specified stream and back-insert into the given field buffers.
- Template Parameters
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- Parameters
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Additional requirements