exon 0.32.4

A platform for scientific data processing and analysis.
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56

// Copyright 2024 WHERE TRUE Technologies.
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//     http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.

use arrow::array::StringArray;
use bytes::Bytes;
use datafusion::datasource::file_format::write::BatchSerializer;
use noodles::fasta::{
    record::{Definition, Sequence},
    Record,
};

use super::columns_from_batch::get_array_column;

#[derive(Debug, Default)]
pub(crate) struct FASTASerializer {}

impl BatchSerializer for FASTASerializer {
    fn serialize(
        &self,
        batch: arrow::array::RecordBatch,
        _initial: bool,
    ) -> datafusion::error::Result<bytes::Bytes> {
        let ids = get_array_column::<StringArray>(&batch, "id")?;
        let descriptions = get_array_column::<StringArray>(&batch, "description")?;
        let sequences = get_array_column::<StringArray>(&batch, "sequence")?;

        let b = Vec::new();
        let mut fasta_writer = noodles::fasta::writer::Writer::new(b);

        for i in 0..batch.num_rows() {
            let id = ids.value(i);
            let description = descriptions.value(i);
            let sequence = sequences.value(i);

            let definition = Definition::new(id, Some(Vec::from(description)));
            let sequence = Sequence::from(Vec::from(sequence));

            let record = Record::new(definition, sequence);
            fasta_writer.write_record(&record)?;
        }

        // todo benchmark this
        Ok(Bytes::from(fasta_writer.get_ref().to_vec()))
    }
}