biocommons_bioutils/assemblies/
mod.rs

1//! Static data.
2
3use std::io::Read;
4
5use enum_map::{enum_map, Enum, EnumMap};
6use flate2::read::GzDecoder;
7use serde::Deserialize;
8
9const GRCH37_JSON_GZ: &[u8] = include_bytes!("_data/GRCh37.json.gz");
10const GRCH37_P10_JSON_GZ: &[u8] = include_bytes!("_data/GRCh37.p10.json.gz");
11const GRCH38_JSON_GZ: &[u8] = include_bytes!("_data/GRCh38.json.gz");
12
13#[derive(Debug, Deserialize, Enum, Clone, Copy, PartialEq, Eq, Hash)]
14pub enum Assembly {
15    Grch37,
16    Grch37p10,
17    Grch38,
18}
19
20impl Assembly {
21    /// Deserialize assembly info from embedded compressed JSON.
22    fn load_assembly_info(&self) -> AssemblyInfo {
23        let payload = match self {
24            Assembly::Grch37 => GRCH37_JSON_GZ,
25            Assembly::Grch37p10 => GRCH37_P10_JSON_GZ,
26            Assembly::Grch38 => GRCH38_JSON_GZ,
27        };
28        let mut d = GzDecoder::new(payload);
29        let mut grch37_json = String::new();
30        d.read_to_string(&mut grch37_json)
31            .expect("should not happen; invalid gzip in embedded data");
32        serde_json::from_str::<AssemblyInfo>(&grch37_json)
33            .expect("should not happen; invalid JSON in embedded data")
34    }
35}
36
37#[derive(Debug, Deserialize)]
38pub struct Sequence {
39    pub aliases: Vec<String>,
40    pub assembly_unit: String,
41    pub genbank_ac: String,
42    pub length: usize,
43    pub name: String,
44    pub refseq_ac: String,
45    pub relationship: String,
46    pub sequence_role: String,
47}
48
49#[derive(Debug, Deserialize)]
50pub struct AssemblyInfo {
51    pub date: String,
52    pub description: String,
53    pub genbank_ac: String,
54    pub name: String,
55    pub refseq_ac: String,
56    pub sequences: Vec<Sequence>,
57    pub submitter: String,
58}
59
60lazy_static::lazy_static! {
61    /// Provide information about the assemblies.
62    pub static ref ASSEMBLY_INFOS: EnumMap<Assembly, AssemblyInfo> = enum_map! {
63        Assembly::Grch37 => Assembly::Grch37.load_assembly_info(),
64        Assembly::Grch37p10 => Assembly::Grch37p10.load_assembly_info(),
65        Assembly::Grch38 => Assembly::Grch38.load_assembly_info(),
66    };
67}
68
69#[cfg(test)]
70mod test {
71    use pretty_assertions::assert_eq;
72
73    use crate::assemblies::{Assembly, ASSEMBLY_INFOS};
74
75    #[test]
76    fn smoke() {
77        assert_eq!(ASSEMBLY_INFOS[Assembly::Grch37].sequences.len(), 92);
78        assert_eq!(ASSEMBLY_INFOS[Assembly::Grch37p10].sequences.len(), 275);
79        assert_eq!(ASSEMBLY_INFOS[Assembly::Grch38].sequences.len(), 455);
80    }
81}
82
83// <LICENSE>
84// Copyright 2023 biocommons-bioutils-rs Contributors
85// Copyright 2014 Bioutils Contributors
86//
87// Licensed under the Apache License, Version 2.0 (the "License");
88// you may not use this file except in compliance with the License.
89// You may obtain a copy of the License at
90//
91//     http://www.apache.org/licenses/LICENSE-2.0
92//
93// Unless required by applicable law or agreed to in writing, software
94// distributed under the License is distributed on an "AS IS" BASIS,
95// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
96// See the License for the specific language governing permissions and
97// limitations under the License.
98// </LICENSE>
biocommons_bioutils/assemblies/mod.rs

biocommons_bioutils/assemblies/
mod.rs
