SeqAn3 3.4.0-rc.3
The Modern C++ library for sequence analysis.
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Structured sequence files contain intra-molecular interactions of RNA or protein. Usually, but not necessarily, they contain the nucleotide or amino acid sequences and descriptions as well. Interactions can be represented either as fixed secondary structure, where every character is assigned at most one interaction partner (structure of minimum free energy), or an annotated sequence, where every character is assigned a set of interaction partners with specific base pair probabilities.
The structured sequence file abstraction supports reading ten different fields:
The first three fields are retrieved by default (and in that order). The seqan3::field::structured_seq may be selected to have sequence and structure directly stored in a more memory-efficient combined container. If you select this field you must not select seqan3::field::seq or seqan3::field::structure.
This class comes with two constructors, one for construction from a file name and one for construction from an existing stream and a known format. The first one automatically picks the format based on the extension of the file name. The second can be used if you have a non-file stream, like std::cin or std::istringstream, that you want to read from and/or if you cannot use file-extension based detection, but know that your input file has a certain format.
In most cases the template parameters are deduced completely automatically, e.g. reading from a std::istringstream:
Note that this is not the same as writing structure_file_input<>
(with angle brackets). In the latter case they are explicitly set to their default values, in the former case automatic deduction happens which chooses different parameters depending on the constructor arguments. For opening from file, structure_file_input<>
would have also worked, but for opening from stream it would not have.
In some cases, you do need to specify the arguments, e.g. if you want to read amino acids:
You can define your own traits type to further customise the types used by and returned by this class, see seqan3::structure_file_default_traits_rna for more details. As mentioned above, specifying at least one template parameter yourself means that you loose automatic deduction so if you want to read amino acids and want to read from a string stream you need to give all types yourself:
You can iterate over this file record-wise:
In the above example, rec has the type seqan3::structure_file_input::record_type which is a specialisation of seqan3::record and behaves like a std::tuple (that's why we can access it via get). Instead of using the seqan3::field based interface on the record, you could also use std::get<0>
or even std::get<rna4_vector>
to retrieve the sequence, but it is not recommended, because it is more error-prone.
Note: It is important to write auto &
and not just auto
, otherwise you will copy the record on every iteration. Since the buffer gets "refilled" on every iteration, you can also move the data out of the record if you want to store it somewhere without copying:
Instead of using get
on the record, you can also use structured bindings to decompose the record into its elements:
In this case you immediately get the three elements of the tuple: seq
of seqan3::structure_file_input::seq_type, id
of seqan3::structure_file_input::id_type and structure
of seqan3::structure_file_input::structure_type. But beware: with structured bindings you do need to get the order of elements correctly!
If you want to skip specific fields from the record you can pass a non-empty fields trait object to the structure_file_input constructor to select the fields that should be read from the input. For example to choose a combined field for SEQ and STRUCTURE (see above). Or to never actually read the STRUCTURE, if you don't need it. The following snippets demonstrate the usage of such a fields trait object.
When reading a file, all fields not present in the file (but requested implicitly or via the selected_field_ids
parameter) are ignored.
Since SeqAn files are ranges, you can also create views over files. A useful example is to filter the records based on certain criteria, e.g. minimum length of the sequence field:
You can check whether a file is at end by comparing begin() and end() (if they are the same, the file is at end).
Currently, the only implemented format is seqan3::format_vienna. More formats will follow soon.