data-beans 0.12.0

Sparse genomics data backends, QC, algorithms, and simulation
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

use log::info;

use crate::handlers::explore::off_screen;
use crate::interactive::ui::Tui;
use legume_numeric::matrix::traits::RunningStatOps;

#[path = "import_preview.rs"]
mod import;

// The `from-*` commands `data_beans::import` builds live in `imports`.
mod from_fragments;
mod from_zarr;
mod imports;

pub use from_fragments::*;
pub use from_zarr::*;
pub use imports::*;

////////////////////////////////////////////////////////////////////
// Shared helpers used across all build-from-* subcommands.       //
// Each subcommand lives in its own submodule (`from_*`); helpers //
// that are reused by more than one of them stay here.            //
////////////////////////////////////////////////////////////////////

/// What `--do-squeeze` asks of a build.
#[derive(Debug, Clone, Copy)]
pub(super) struct Squeeze {
    pub(super) on: bool,
    /// The cutoffs, kept while `on` is off so the preview can turn it on.
    pub(super) cut: crate::import::Squeeze,
}

impl Squeeze {
    /// `--do-squeeze`, `--row-nnz-cutoff`, `--column-nnz-cutoff`,
    /// `--block-size`.
    pub(super) fn new(on: bool, rows: usize, columns: usize, block_size: Option<usize>) -> Self {
        let cut = crate::import::Squeeze {
            rows,
            columns,
            block_size,
        };
        Self { on, cut }
    }

    /// The library's squeeze, when on.
    fn cut(self) -> Option<crate::import::Squeeze> {
        self.on.then_some(self.cut)
    }

    fn apply(self, backend_file: &str) -> anyhow::Result<()> {
        match self.cut() {
            Some(cut) => cut.apply(backend_file),
            None => Ok(()),
        }
    }
}

/// Build with `whole`, the library's import squeezed as asked and put in
/// place, or, on a terminal, `stage` it and keep it after the import
/// preview ([`keep_import`]).
pub(super) fn run_import<O>(
    command: &str,
    session: Option<&legume_tui::Session>,
    opts: &O,
    out: crate::import::Output,
    squeeze: Squeeze,
    whole: fn(&O, &crate::import::Output) -> anyhow::Result<Box<str>>,
    stage: fn(&O, &crate::import::Output) -> anyhow::Result<crate::import::Staged>,
) -> anyhow::Result<()> {
    if session.is_none() {
        let squeeze = squeeze.cut();
        whole(opts, &crate::import::Output { squeeze, ..out })?;
    } else {
        let staged = stage(opts, &out)?;
        if keep_import(command, session, squeeze, staged.working())? {
            staged.finish()?;
        } else {
            staged.discard()?;
        }
    }
    Ok(())
}

/// The end of a build, before the output is finalized: squeezed as asked,
/// or, with a `session` (on a terminal), the import preview first: the
/// rows' and columns' non-zeros as histograms against the squeeze cutoffs,
/// each a setting. Enter keeps the build (squeezed when on); `q`
/// discards it. Whether to keep it: false for the caller to delete it
/// ([`crate::import::remove_build`]).
pub(super) fn keep_import(
    command: &str,
    session: Option<&legume_tui::Session>,
    squeeze: Squeeze,
    backend_file: &str,
) -> anyhow::Result<bool> {
    let Some(session) = session else {
        squeeze.apply(backend_file)?;
        return Ok(true);
    };
    let mut tui = Tui::new(session);
    let (rows, columns) = off_screen(Some(&mut tui), || nnz_by_axis(backend_file))?;
    let Some(s) = import::preview(&mut tui, command, backend_file, &rows, &columns, squeeze)?
    else {
        info!("{command}: discarded");
        return Ok(false);
    };
    off_screen(Some(&mut tui), || s.apply(backend_file))?;
    Ok(true)
}

/// Non-zeros per row and per column of the backend at `file`: off its
/// indexes, else counted in a pass.
fn nnz_by_axis(file: &str) -> anyhow::Result<(Vec<usize>, Vec<usize>)> {
    let data = crate::sparse_io::open_sparse_matrix_by_path(file)?;
    let counts = |p: &[u64], n: usize| -> Option<Vec<usize>> {
        (p.len() == n + 1).then(|| p.windows(2).map(|w| (w[1] - w[0]) as usize).collect())
    };
    let as_counts = |v: Vec<f32>| -> Vec<usize> { v.into_iter().map(|n| n as usize).collect() };
    let (nrow, ncol) = (
        data.num_rows().unwrap_or(0),
        data.num_columns().unwrap_or(0),
    );
    let rows = match counts(data.row_indptr(), nrow) {
        Some(c) => c,
        None => as_counts(crate::qc::collect_row_stat(data.as_ref(), None)?.count_positives()),
    };
    let columns = match counts(data.column_indptr(), ncol) {
        Some(c) => c,
        None => as_counts(crate::qc::collect_column_stat(data.as_ref(), None)?.count_positives()),
    };
    Ok((rows, columns))
}