oxbow 0.7.0

Read conventional genomic file formats as data frames and more via Apache Arrow.
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

use std::io::{Read, Seek};

use arrow::error::ArrowError;
use arrow::record_batch::RecordBatch;
use arrow::record_batch::RecordBatchReader;
use bigtools::{BigBedRead, BigWigRead, ZoomIntervalError, ZoomRecord};
use noodles::core::region::Region;

use crate::batch::{Push as _, RecordBatchBuilder as _};
use crate::bbi::model::zoom::{BBIZoomRecord, BatchBuilder};

/// An iterator yielding BBI zoom record batches that intersect a genomic range.
pub struct BatchIterator {
    builder: BatchBuilder,
    entries: Box<dyn Iterator<Item = Result<(String, ZoomRecord), ZoomIntervalError>> + Send>,
    batch_size: usize,
    limit: usize,
    count: usize,
}

impl BatchIterator {
    pub fn from_bigwig<R: Read + Seek + Send + 'static>(
        reader: BigWigRead<R>,
        region: Region,
        level: u32,
        builder: BatchBuilder,
        batch_size: usize,
        limit: Option<usize>,
    ) -> Self {
        let chrom = region.name().to_string();
        let chrominfo: Vec<_> = reader
            .chroms()
            .iter()
            .map(|item| (item.name.clone(), item.length))
            .collect();
        let length = chrominfo
            .iter()
            .find(|(name, _)| *name == chrom)
            .map(|(_, length)| length)
            .unwrap();
        let interval = region.interval();
        let start = interval
            .start()
            .map(|pos| usize::from(pos) as u32)
            .unwrap_or(1)
            - 1;
        let end = interval
            .end()
            .map(|pos| usize::from(pos) as u32)
            .unwrap_or_else(|| *length);
        let iter = reader
            .get_zoom_interval_move(&chrom, start, end, level)
            .unwrap()
            .map(move |result| {
                result
                    .map(|record| (chrom.clone(), record))
                    .map_err(ZoomIntervalError::BBIReadError)
            });
        Self {
            builder,
            entries: Box::new(iter),
            batch_size,
            limit: limit.unwrap_or(usize::MAX),
            count: 0,
        }
    }

    pub fn from_bigbed<R: Read + Seek + Send + 'static>(
        reader: BigBedRead<R>,
        region: Region,
        level: u32,
        builder: BatchBuilder,
        batch_size: usize,
        limit: Option<usize>,
    ) -> Self {
        let chrom = region.name().to_string();
        let chrominfo: Vec<_> = reader
            .chroms()
            .iter()
            .map(|item| (item.name.clone(), item.length))
            .collect();
        let length = chrominfo
            .iter()
            .find(|(name, _)| *name == chrom)
            .map(|(_, length)| length)
            .unwrap();
        let interval = region.interval();
        let start = interval
            .start()
            .map(|pos| usize::from(pos) as u32)
            .unwrap_or(1)
            - 1;
        let end = interval
            .end()
            .map(|pos| usize::from(pos) as u32)
            .unwrap_or_else(|| *length);
        let iter = reader
            .get_zoom_interval_move(&chrom, start, end, level)
            .unwrap()
            .map(move |result| {
                result
                    .map(|record| (chrom.clone(), record))
                    .map_err(ZoomIntervalError::BBIReadError)
            });
        Self {
            builder,
            entries: Box::new(iter),
            batch_size,
            limit: limit.unwrap_or(usize::MAX),
            count: 0,
        }
    }
}

impl Iterator for BatchIterator {
    type Item = Result<RecordBatch, ArrowError>;

    fn next(&mut self) -> Option<Self::Item> {
        let mut count = 0;

        while count < self.batch_size && self.count < self.limit {
            match self.entries.next() {
                Some(Ok((chrom, entry))) => {
                    let record = BBIZoomRecord::new(&chrom, &entry);
                    match self.builder.push(&record) {
                        Ok(()) => {
                            self.count += 1;
                            count += 1;
                        }
                        Err(e) => return Some(Err(e.into())),
                    }
                }
                Some(Err(e)) => return Some(Err(ArrowError::ExternalError(e.into()))),
                None => break,
            }
        }

        if count == 0 {
            None
        } else {
            let batch = self.builder.finish();
            Some(batch)
        }
    }
}

impl RecordBatchReader for BatchIterator {
    fn schema(&self) -> arrow::datatypes::SchemaRef {
        self.builder.schema()
    }
}