The GenBank format (tag). More...
#include <seqan3/io/sequence_file/format_genbank.hpp>
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... | |
The GenBank format (tag).
genbank is the format used in GenBank sequence database. See (http://quma.cdb.riken.jp/help/gbHelp.html) for a an in-depth description of the format.
The genbank format provides the fields seqan3::field::SEQ and seqan3::field::ID. Both fields are required when writing.
There is no truncate_ids option while reading because the GenBank format has no (FASTA-like) idbuffer. Instead, there is the option "complete_header" to indicate whether the whole header is to be read (embl_genbank_complete_header=true) or only the "LOCUS" information should be stored.
Qualities passed to the write function are ignored.
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related |
Read from the specified stream and back-insert into the given field buffers.
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. |
[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. |
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related |
Write the given fields to the specified stream.
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. |
[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. |
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inlinestatic |
The valid file extensions for this format; note that you can modify this value.