seqan3::format_embl Struct Reference

The EMBL format (tag). More...

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

Inheritance diagram for seqan3::format_embl:

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 EMBL format (tag).

Introduction

embl is the format used in ENA sequence records. See the (ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/usrman.txt) for a an in-depth description of the format.

Fields

The embl 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 ID is read until the stream encounters a ';'. Unless, the option truncate_ids is set to true, then the id is read until it either sees a blank, ';' or a new line. When the option "embl_genbank_complete_header" is set to true (Default: false) the whole header is read into the id.

When writing the ID-line, the sequence length is appended.

All other identifiers apart from 'ID' and 'SQ' are currently ignored.

Passed qualities to either the read or write function are ignored.

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_embl::file_extensions

inlinestatic

Initial value:

{
        { "embl" },
    }

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_embl.hpp