exon-gff 0.9.1

A library for reading and writing GFF files with Exon.
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
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158

// Copyright 2023 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 std::{str::FromStr, sync::Arc};

use arrow::{error::ArrowError, error::Result as ArrowResult, record_batch::RecordBatch};

use futures::Stream;
use tokio::io::{AsyncBufRead, AsyncBufReadExt};

use super::{array_builder::GFFArrayBuilder, GFFConfig};

/// Reads a GFF file into arrow record batches.
pub struct BatchReader<R> {
    /// The reader to read from.
    reader: R,

    /// The configuration for this reader.
    config: Arc<GFFConfig>,

    /// A region to filter on.
    region: Option<Arc<noodles::core::Region>>,
}

impl<R> BatchReader<R>
where
    R: AsyncBufRead + Unpin + Send,
{
    pub fn new(reader: R, config: Arc<GFFConfig>) -> Self {
        Self {
            reader,
            config,
            region: None,
        }
    }

    pub fn with_region(mut self, region: Arc<noodles::core::Region>) -> Self {
        self.region = Some(region);
        self
    }

    pub fn into_stream(self) -> impl Stream<Item = Result<RecordBatch, ArrowError>> {
        futures::stream::unfold(self, |mut reader| async move {
            match reader.read_batch().await {
                Ok(Some(batch)) => Some((Ok(batch), reader)),
                Ok(None) => None,
                Err(e) => Some((Err(ArrowError::ExternalError(Box::new(e))), reader)),
            }
        })
    }

    async fn read_line(&mut self) -> std::io::Result<Option<noodles::gff::Line>> {
        loop {
            let mut buf = String::new();
            match self.reader.read_line(&mut buf).await {
                Ok(0) => return Ok(None),
                Ok(_) => {
                    buf.pop();

                    #[cfg(target_os = "windows")]
                    if buf.ends_with('\r') {
                        buf.pop();
                    }

                    let line = match noodles::gff::Line::from_str(&buf) {
                        Ok(line) => line,
                        Err(e) => match e {
                            noodles::gff::line::ParseError::InvalidDirective(_) => {
                                continue;
                            }
                            noodles::gff::line::ParseError::InvalidRecord(e) => {
                                return Err(std::io::Error::new(
                                    std::io::ErrorKind::InvalidData,
                                    format!("invalid record: {buf} error: {e}"),
                                ))
                            }
                        },
                    };
                    buf.clear();
                    return Ok(Some(line));
                }
                Err(e) => return Err(e),
            };
        }
    }

    fn filter(&self, record: &noodles::gff::Record) -> Result<bool, ArrowError> {
        let chrom = record.reference_sequence_name();

        match &self.region {
            Some(region) => {
                let region_name = std::str::from_utf8(region.name())?;

                if chrom != region_name {
                    return Ok(false);
                }

                if !region.interval().contains(record.start()) {
                    return Ok(false);
                }

                Ok(true)
            }
            None => Ok(true),
        }
    }

    async fn read_batch(&mut self) -> ArrowResult<Option<RecordBatch>> {
        let mut gff_array_builder = GFFArrayBuilder::new();
        let mut batch_size = 0;

        loop {
            match self.read_line().await? {
                None => break,
                Some(line) => match line {
                    noodles::gff::Line::Comment(_) => {}
                    noodles::gff::Line::Directive(_) => {}
                    noodles::gff::Line::Record(record) => {
                        // Filter on region if provided.
                        if !self.filter(&record)? {
                            continue;
                        }

                        gff_array_builder.append(&record)?;
                        batch_size += 1;

                        if batch_size == self.config.batch_size {
                            break;
                        }
                    }
                },
            }
        }

        if gff_array_builder.is_empty() {
            return Ok(None);
        }

        let batch =
            RecordBatch::try_new(self.config.file_schema.clone(), gff_array_builder.finish())?;

        match &self.config.projection {
            Some(projection) => Ok(Some(batch.project(projection)?)),
            None => Ok(Some(batch)),
        }
    }
}