seqan3::format_fasta Struct Reference

The FastA format (tag). More...

#include <seqan3/io/sequence_file/format_fasta.hpp>

Inheritance diagram for seqan3::format_fasta:

Static Public Attributes
static std::vector< std::string >	file_extensions
	The valid file extensions for this format; note that you can modify this value. More...

Related Functions
(Note that these are not member functions.)
Requirements for seqan3::SequenceFileInputFormat
You can expect these members on all types that implement seqan3::SequenceFileInputFormat.
void	read (stream_type &stream, seqan3::sequence_file_input_options const &options, seq_type &sequence, id_type &id, qual_type &qualities)
	Read from the specified stream and back-insert into the given field buffers. More...
Requirements for seqan3::SequenceFileOutputFormat
You can expect these members on all types that implement seqan3::SequenceFileOutputFormat.
void	write (stream_type &stream, seqan3::sequence_file_output_options const &options, seq_type &&sequence, id_type &&id, qual_type &&qualities)
	Write the given fields to the specified stream. More...

Detailed Description

The FastA format (tag).

Introduction

FastA is the de-facto-standard for sequence storage in bionformatics. See the article on wikipedia for a an in-depth description of the format.

Fields

The FastA format provides the fields seqan3::field::SEQ and seqan3::field::ID. Both fields are required when writing.

Implementation notes

When reading the ID-line the identifier (either ; or >) and any blank characters before the actual ID are stripped.

This implementation supports the following less known and optional features of the format:

• ID lines beginning with ; instead of >
• line breaks and other whitespace characters in any part of the sequence
• character counts within the sequence (they are simply ignored)

The following optional features are currently not supported:

• Multiple comment lines (starting with either ; or >), only one ID line before the sequence line is accepted

Friends And Related Function Documentation

read()

void read ( stream_type &  stream, seqan3::sequence_file_input_options const &  options, seq_type &  sequence, id_type &  id, qual_type &  qualities  )

related

Read from the specified stream and back-insert into the given field buffers.

Template Parameters

stream_type	Input stream, must satisfy seqan3::IStream with char.
seq_type	Type of the seqan3::field::SEQ input; must satisfy std::ranges::OutputRange over a seqan3::Alphabet.
id_type	Type of the seqan3::field::ID input; must satisfy std::ranges::OutputRange over a seqan3::Alphabet.
qual_type	Type of the seqan3::field::QUAL input; must satisfy std::ranges::OutputRange over a seqan3::WritableQualityAlphabet.

Parameters

[in,out]	stream	The input stream to read from.
[in]	options	File specific options passed to the format.
[out]	sequence	The buffer for seqan3::field::SEQ input, i.e. the "sequence".
[out]	id	The buffer for seqan3::field::ID input, e.g. the header line in FastA.
[out]	qualities	The buffer for seqan3::field::QUAL input.

Additional requirements

• The function must also accept std::ignore as parameter for any of the fields. [This is enforced by the concept checker!]
• In this case the data read for that field shall be discarded by the format.
• Instead of passing the fields seqan3::field::SEQ and seqan3::field::QUAL, you may also pass seqan3::field::SEQ_QUAL to both parameters. If you do, the seqan3::value_type_t of the argument must be a specialisation of seqan3::qualified and the second template parameter to seqan3::sequence_file_input_options must be set to true.

write()

void write ( stream_type &  stream, seqan3::sequence_file_output_options const &  options, seq_type &&  sequence, id_type &&  id, qual_type &&  qualities  )

related

Write the given fields to the specified stream.

Template Parameters

stream_type	Output stream, must satisfy seqan3::OStream with char.
seq_type	Type of the seqan3::field::SEQ output; must satisfy std::ranges::OutputRange over a seqan3::Alphabet.
id_type	Type of the seqan3::field::ID output; must satisfy std::ranges::OutputRange over a seqan3::Alphabet.
qual_type	Type of the seqan3::field::QUAL output; must satisfy std::ranges::OutputRange over a seqan3::QualityAlphabet.

Parameters

[in,out]	stream	The output stream to write into.
[in]	options	File specific options passed to the format.
[in]	sequence	The data for seqan3::field::SEQ, i.e. the "sequence".
[in]	id	The data for seqan3::field::ID, e.g. the header line in FastA.
[in]	qualities	The data for seqan3::field::QUAL.

Additional requirements

• The format must also accept std::ignore as parameter for any of the fields, however it shall throw an exception if one of the fields required for writing the format is marked as such. [this shall be checked inside the function]
• The format does not handle seqan3::field::SEQ_QUAL, instead seqan3::sequence_file_output splits it into two views and passes it to the format as if they were separate.

Member Data Documentation

file_extensions

std::vector<std::string> seqan3::format_fasta::file_extensions

inlinestatic

Initial value:

{
        { "fasta" },
        { "fa"    },
        { "fna"   },
        { "ffn"   },
        { "faa"   },
        { "frn"   },
    }

The valid file extensions for this format; note that you can modify this value.

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The documentation for this struct was generated from the following file:

• seqan3/io/sequence_file/format_fasta.hpp