seqan3::format_fasta Class Reference

The FASTA format. More...

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

Inheritance diagram for seqan3::format_fasta:

Public Member Functions
Constructors, destructor and assignment
	format_fasta () noexcept=default
	Defaulted.
	format_fasta (format_fasta const &) noexcept=default
	Defaulted.
format_fasta &	operator= (format_fasta const &) noexcept=default
	Defaulted.
	format_fasta (format_fasta &&) noexcept=default
	Defaulted.
format_fasta &	operator= (format_fasta &&) noexcept=default
	Defaulted.
	~format_fasta () noexcept=default
	Defaulted.

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

Protected Member Functions
template<typename stream_type , typename legal_alph_type , typename stream_pos_type , typename seq_type , typename id_type , typename qual_type >
void	read_sequence_record (stream_type &stream, sequence_file_input_options< legal_alph_type > const &options, stream_pos_type &position_buffer, seq_type &sequence, id_type &id, qual_type &qualities)
	Read from the specified stream and back-insert into the given field buffers.
template<typename stream_type , typename seq_type , typename id_type , typename qual_type >
void	write_sequence_record (stream_type &stream, sequence_file_output_options const &options, seq_type &&sequence, id_type &&id, qual_type &&qualities)
	Write the given fields to the specified stream.

Additional Inherited Members
Related Symbols inherited from seqan3::sequence_file_input_format< t >
void	read_sequence_record (stream_type &stream, seqan3::sequence_file_input_options const &options, stream_pos_type &position_buffer, seq_type &sequence, id_type &id, qual_type &qualities)
	Read from the specified stream and back-insert into the given field buffers.
static inline std::vector< std::string >	file_extensions
	The format type is required to provide a vector of all supported file extensions.
Related Symbols inherited from seqan3::sequence_file_output_format< t >
static inline std::vector< std::string >	file_extensions
	The format type is required to provide a vector of all supported file extensions.

Detailed Description

The FASTA format.

Introduction

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

fields_specialisation

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

Remarks

For a complete overview, take a look at Sequence File

Member Function Documentation

read_sequence_record()

template<typename stream_type , typename legal_alph_type , typename stream_pos_type , typename seq_type , typename id_type , typename qual_type >

void seqan3::format_fasta::read_sequence_record ( stream_type &  stream, sequence_file_input_options< legal_alph_type > const &  options, stream_pos_type &  position_buffer, seq_type &  sequence, id_type &  id, qual_type &  qualities  )

inlineprotected

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

Template Parameters

stream_type	Input stream, must satisfy seqan3::input_stream_over with char.
stream_pos_type	Buffer for storing the current record's file position.
seq_type	Type of the seqan3::field::seq input; must satisfy std::ranges::output_range over a seqan3::alphabet.
id_type	Type of the seqan3::field::id input; must satisfy std::ranges::output_range over a seqan3::alphabet.
qual_type	Type of the seqan3::field::qual input; must satisfy std::ranges::output_range over a seqan3::writable_quality_alphabet.

Parameters

[in,out]	stream	The input stream to read from.
[in,out]	position_buffer	The buffer to store the current record's file position.
[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.

write_sequence_record()

template<typename stream_type , typename seq_type , typename id_type , typename qual_type >

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

inlineprotected

Write the given fields to the specified stream.

Template Parameters

stream_type	Output stream, must satisfy seqan3::output_stream_over with char.
seq_type	Type of the seqan3::field::seq output; must satisfy std::ranges::output_range over a seqan3::alphabet.
id_type	Type of the seqan3::field::id output; must satisfy std::ranges::output_range over a seqan3::alphabet.
qual_type	Type of the seqan3::field::qual output; must satisfy std::ranges::output_range over a seqan3::quality_alphabet.

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]

Implements seqan3::sequence_file_output_format< t >.

Member Data Documentation

file_extensions

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

inlinestatic

Initial value:

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

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

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

• format_fasta.hpp