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SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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Learning Objective:
You will get an overview of how Input/Output files are handled in SeqAn and learn how to read and write sequence files. This tutorial is a walk-through with links into the API documentation and also meant as a source for copy-and-paste code.
| Difficulty | Easy |
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| Duration | 90 min |
| Prerequisite tutorials | Setup, Ranges, Alphabets |
| Recommended reading |
Most file formats in bioinformatics are structured as lists of records. In SeqAn we model our files as a range over records. This interface allows us to easily stream over a file, apply filters and convert formats, sometimes only in a single line of code. The file format is automatically detected by the file name extension and compressed files can be handled without any effort. We can even stream over files in a python-like way with range-based for loops:
We will explain the details about reading and writing files in the Sequence File section below. Currently, SeqAn supports the following file formats:
.gz files and libbz2 for reading .bz2 files. You can check whether you have installed these libraries by running cmake . in your build directory. If -- Optional dependency: ZLIB-x.x.x found. is displayed on the command line then you can read/write compressed files in your programs.Before we dive into the details, we will outline the general design of our file objects, hoping that it will make the following tutorial easier to understand.
As mentioned above, our file object is a range over records. More specifically, a range over objects of type seqan3::sequence_record.
Output files can handle various types that fulfill the requirements of the format (e.g. a sequence has to be a range over an alphabet). In contrast to this, input files have certain default types for record fields that can be modified via a traits type.
For example, on construction you can specify seqan3::sequence_file_input_default_traits_dna or seqan3::sequence_file_input_default_traits_aa for reading dna (Nucleotide) and protein (Aminoacid) sequences respectively (section File traits will covers this in more detail).
Opening and closing files is also handled automatically. If a file cannot be opened for reading or writing, a seqan3::file_open_error is thrown.
Sequence files are the most generic and common biological files. Well-known formats include FASTA and FASTQ.
A FASTA record contains the sequence id and the sequence characters. Here is an example of a FASTA file:
In SeqAn we provide the seqan3::format_fasta to read sequence files in FASTA format.
A FASTQ record contains an additional quality value for each sequence character. Here is an example of a FASTQ file:
In SeqAn we provide the seqan3::format_fastq to read sequence files in FASTQ format.
An EMBL record stores sequence and its annotation together. We are only interested in the id (ID) and sequence (SQ) information for a sequence file. Qualities are not stored in this format. Here is an example of an EMBL file:
In SeqAn we provide the seqan3::format_embl to read sequence files in EMBL format.
The formerly introduced formats can be identified by the following file name extensions (this is important for automatic format detection from a file name as you will learn in the next section).
| File Format | SeqAn format class | File Extensions |
|---|---|---|
| FASTA | seqan3::format_fasta | .fa, .fasta, .fna, .ffn, .ffa, .frn |
| FASTQ | seqan3::format_fastq | .fq, .fastq |
| EMBL | seqan3::format_embl | .embl |
You can access the valid file extensions via the file_extensions member variable in a format and you can also customise this list if you want to allow different or additional file extensions:
The Sequence file abstraction supports reading three different fields:
The three fields are retrieved by default.
You can include the SeqAn sequence file functionality with:
At first, you need to construct a seqan3::sequence_file_input object that handles file access. In most cases, you construct from a file name, but you can also construct a sequence file object directly from a stream (e.g. std::cin or std::stringstream), but then you need to know your format beforehand:
All template parameters of the seqan3::sequence_file_input are automatically deduced, even the format! We detect the format by the file name extension. The file extension in the example above is .fasta so we choose the seqan3::format_fasta.
The seqan3::sequence_file_input needs to know the types of the data you are reading in (e.g. that your sequence is a dna sequence) at compile-time. These necessary types are defined in the traits type argument (seqan3::sequence_file_input::traits_type) which by default is set to seqan3::sequence_file_input_default_traits_dna.
We thereby assume that
In case you want to read a protein sequence instead, we also provide the seqan3::sequence_file_input_default_traits_aa traits type which sets the seqan3::sequence_record::sequence field to a std::vector over the seqan3::aa27 alphabet.
You can specify the traits object as the first template argument for the sequence file:
You can also customise the types by inheriting from one of the default traits and changing the type manually. See the detailed information on seqan3::sequence_file_input_default_traits_dna for an example.
After construction, you can now read the seqan3::sequence_record's. As described in the basic file layout, our file objects behave like ranges so you can use a range based for loop to conveniently iterate over the file:
In the above example, record has the type seqan3::sequence_file_input::record_type which is seqan3::sequence_record.
auto & and not just auto, otherwise you will copy the record on every iteration.You can read up more on the different ways to stream over the file object in the detailed documentation of seqan3::sequence_file_input.
and then create a simple program that reads in all the records from that file and prints the id, sequence and quality information to the command line using the seqan3::debug_stream. Access the record via the member accessor of seqan3::sequence_record!
Note: you include the seqan3::debug_stream with the following header
The code will print the following:
In the examples above, we always use auto to deduce the record type automatically. In case you need the type explicitly, e.g. if you want to store the records in a variable, you can access the type member seqan3::sequence_file_input::record_type.
You can move the record out of the file if you want to store it somewhere without copying.
Create a small program that reads in a FASTA file and stores all the records in a std::vector.
After reading, print the vector (this works natively with the seqan3::debug_stream).
Test your program with the following file:
It should print the following:
Note that the quality (third element in the triple) is empty because we are reading a FASTA file.
Since SeqAn files are ranges, you can also create views over files. This enables us to create solutions for lots of use cases using only a few lines of code.
A common use case is to read chunks from a file instead of the whole file at once or line by line.
You can do so easily on a file range by using the seqan3::views::chunk.
The example above will iterate over the file by reading 10 records at a time. If no 10 records are available any more, it will just print the remaining records.
On some occasions, you are only interested in sequence records that fulfill a certain criteria, e.g. having a minimum sequence length or a minimum average quality. Just like in the example with seqan3::views::chunk you can use std::ranges::filter for this purpose:
To remind you what you have learned in the Ranges tutorial before, a view is not applied immediately but lazy evaluated. That means your file is still parsed record by record and not at once.
In modern Next Generation Sequencing experiments, you often encounter paired-end read data which is split into two files. The read pairs are identified by their identical id and position in the files.
If you want to handle one pair of reads at a time, you can do so easily with a seqan3::views::zip.
Implement a small program that reads in a FASTQ file and prints the first 2 sequences that have a length of at least 5.
Hints:
std::ranges::size to retrieve the size of a range.std::views::filter and std::views::take Test your program on the following FASTQ file:
It should output seq1 and seq3.
You construct the seqan3::sequence_file_output just like the seqan3::sequence_file_input by giving it a file name or a stream.
Writing to std::cout:
The easiest way to write to a sequence file is to use the seqan3::sequence_file_output::push_back() member function. It works similarly to how it works on a std::vector.
Use your code (or the solution) from the previous assignment. Iterate over the records with a for loop and instead of just printing the ids, write out all the records that satisfy the filter to a new file called output.fastq.
Test your code on the same FASTQ file. The file output.fastq should contain the following records:
Again we want to point out the convenient advantage of modelling files as ranges. The seqan3::sequence_file_input models std::ranges::input_range and in the "reading a file" section you already saw a few examples of how to pipe a view onto such a range. The output files model std::ranges::output_range. This allows us to use ranges algorithms like std::ranges::move to "move" records from input to output files.
Working on your solution from the previous assignment, try to remove the for loop in favour of a std::ranges algorithm.
The result should be the same.
As mentioned before, the seqan3::sequence_record is shared between formats which allows for easy file conversion. For example you can read in a FASTQ file and output a FASTA file in one line:
Yes, that's it! Of course this only works because all fields that are required in FASTA are provided in FASTQ. The other way around would not work as easily because we have no quality information (and would make less sense too).
1.9.8