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Merge pull request #36 from cauliyang/dev
feat: Update dependencies versions and add new module
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| [package] | ||
| name = "deepbiop-fa" | ||
| version = { workspace = true } | ||
| authors = { workspace = true } | ||
| edition = { workspace = true } | ||
| homepage = { workspace = true } | ||
| repository = { workspace = true } | ||
| keywords = ["parquet", "fasta", "deep-learning"] | ||
| license = { workspace = true } | ||
| readme = "../../README.md" | ||
| description = "Deep Learning Preprocessing Library for Fastq Format" | ||
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| [dependencies] | ||
| thiserror = { workspace = true } | ||
| anyhow = { workspace = true } | ||
| noodles = { workspace = true } | ||
| rayon = { workspace = true } | ||
| log = { workspace = true } | ||
| needletail = { workspace = true } | ||
| ahash = { workspace = true } | ||
| numpy = { workspace = true } | ||
| ndarray = { workspace = true } | ||
| serde = { workspace = true } | ||
| serde_json = { workspace = true } | ||
| derive_builder = { workspace = true } | ||
| itertools = { workspace = true } | ||
| lexical = { workspace = true } | ||
| flate2 = { workspace = true } | ||
| bstr = { workspace = true } | ||
| walkdir = { workspace = true } | ||
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| parquet = { workspace = true } | ||
| arrow = { workspace = true } | ||
| candle-core = { workspace = true } | ||
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| pyo3 = { workspace = true } | ||
| pyo3-stub-gen = { workspace = true } | ||
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| deepbiop-utils = { path = "../deepbiop-utils", version = "0.1" } | ||
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| [dev-dependencies] | ||
| bio = { workspace = true } | ||
| tempfile = { workspace = true } | ||
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| [features] | ||
| python = [] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| use ahash::HashMap; | ||
| use ndarray::{Array2, Array3}; | ||
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| pub type Element = i32; | ||
| pub type Matrix = Array2<Element>; | ||
| pub type Tensor = Array3<Element>; | ||
| pub type Kmer2IdTable = HashMap<Vec<u8>, Element>; | ||
| pub type Id2KmerTable = HashMap<Element, Vec<u8>>; | ||
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| mod option; | ||
| mod parquet; | ||
| mod record; | ||
| mod traits; | ||
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| pub use option::*; | ||
| pub use parquet::*; | ||
| pub use record::*; | ||
| pub use traits::*; |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| use derive_builder::Builder; | ||
| use serde::{Deserialize, Serialize}; | ||
| use std::fmt::{self, Display, Formatter}; | ||
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| use pyo3::prelude::*; | ||
| use pyo3_stub_gen::derive::*; | ||
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| pub const BASES: &[u8] = b"ATCGN"; | ||
| pub const QUAL_OFFSET: u8 = 33; | ||
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| #[gen_stub_pyclass] | ||
| #[pyclass(module = "deepbiop.fa")] | ||
| #[derive(Debug, Builder, Default, Clone, Serialize, Deserialize)] | ||
| pub struct FaEncoderOption { | ||
| #[pyo3(get, set)] | ||
| #[builder(default = "QUAL_OFFSET")] | ||
| pub qual_offset: u8, | ||
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| #[pyo3(get, set)] | ||
| #[builder(default = "BASES.to_vec()")] | ||
| pub bases: Vec<u8>, | ||
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| #[pyo3(get, set)] | ||
| #[builder(default = "2")] | ||
| pub threads: usize, | ||
| } | ||
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| #[gen_stub_pymethods] | ||
| #[pymethods] | ||
| impl FaEncoderOption { | ||
| #[new] | ||
| fn py_new(qual_offset: u8, bases: String, threads: Option<usize>) -> Self { | ||
| FaEncoderOptionBuilder::default() | ||
| .qual_offset(qual_offset) | ||
| .bases(bases.as_bytes().to_vec()) | ||
| .threads(threads.unwrap_or(2)) | ||
| .build() | ||
| .expect("Failed to build FqEncoderOption from Python arguments.") | ||
| } | ||
| } | ||
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| impl Display for FaEncoderOption { | ||
| fn fmt(&self, f: &mut Formatter) -> fmt::Result { | ||
| write!( | ||
| f, | ||
| "FaEncoderOption {{ qual_offset: {}, bases: {:?}}}", | ||
| self.qual_offset, self.bases | ||
| ) | ||
| } | ||
| } |
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