Skip to content

Commit

Permalink
bug fix
Browse files Browse the repository at this point in the history
  • Loading branch information
@kaizhang
kaizhang committed Sep 29, 2024
1 parent 2369f25 commit 1028fb0
Showing 1 changed file with 80 additions and 24 deletions.
104 changes: 80 additions & 24 deletions precellar/src/seqspec.rs
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
use log::warn;
use serde::{Deserialize, Deserializer};
use serde::{Deserialize, Deserializer, Serialize};
use serde_yaml::{self, Value};
use std::{fs, ops::Range, str::FromStr};
use anyhow::{bail, Result};
Expand All @@ -9,7 +9,7 @@ use cached_path::Cache;

use crate::io::open_file_for_read;

#[derive(Deserialize, Debug)]
#[derive(Deserialize, Serialize, Debug)]
pub struct Assay {
pub seqspec_version: String,
pub assay_id: String,
Expand Down Expand Up @@ -38,7 +38,8 @@ impl Assay {
self.sequence_spec.as_ref().expect("sequence_spec is empty")
.iter().filter_map(move |read| if read.modality == modality {
let region = self.get_region_by_modality(modality)?;
let index = read.get_index(region).expect("primer not found");
let index = read.get_index(region)
.expect(&format!("Region: {} does not have Primer: {}", region.region_id, read.primer_id));
Some((read, index))
} else {
None
Expand All @@ -59,7 +60,7 @@ impl Assay {
}
}

#[derive(Deserialize, Debug, Copy, Clone, PartialEq, Eq, Hash)]
#[derive(Deserialize, Serialize, Debug, Copy, Clone, PartialEq, Eq, Hash)]
#[serde(rename_all = "lowercase")]
pub enum Modality {
Dna,
Expand Down Expand Up @@ -92,7 +93,7 @@ pub enum LibraryProtocol {
Custom(Vec<ProtocolItem>),
}

#[derive(Deserialize, Debug)]
#[derive(Deserialize, Serialize, Debug)]
pub struct ProtocolItem {
pub protocol_id: String,
pub name: Option<String>,
Expand All @@ -117,13 +118,25 @@ impl<'de> Deserialize<'de> for LibraryProtocol {
}
}

impl Serialize for LibraryProtocol {
fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
where
S: serde::ser::Serializer
{
match self {
LibraryProtocol::Standard(s) => s.serialize(serializer),
LibraryProtocol::Custom(items) => items.serialize(serializer),
}
}
}

#[derive(Debug)]
pub enum LibraryKit {
Standard(String),
Custom(Vec<KitItem>),
}

#[derive(Deserialize, Debug)]
#[derive(Deserialize, Serialize, Debug)]
pub struct KitItem {
pub kit_id: String,
pub name: Option<String>,
Expand All @@ -148,6 +161,18 @@ impl<'de> Deserialize<'de> for LibraryKit {
}
}

impl Serialize for LibraryKit {
fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
where
S: serde::ser::Serializer
{
match self {
LibraryKit::Standard(s) => s.serialize(serializer),
LibraryKit::Custom(items) => items.serialize(serializer),
}
}
}

#[derive(Debug)]
pub enum SequenceProtocol {
Custom(Vec<ProtocolItem>),
Expand All @@ -172,6 +197,18 @@ impl <'de> Deserialize<'de> for SequenceProtocol {
}
}

impl Serialize for SequenceProtocol {
fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
where
S: serde::ser::Serializer
{
match self {
SequenceProtocol::Standard(s) => s.serialize(serializer),
SequenceProtocol::Custom(items) => items.serialize(serializer),
}
}
}

#[derive(Debug)]
pub enum SequenceKit {
Standard(String),
Expand All @@ -196,7 +233,19 @@ impl<'de> Deserialize<'de> for SequenceKit {
}
}

#[derive(Deserialize, Debug)]
impl Serialize for SequenceKit {
fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
where
S: serde::ser::Serializer
{
match self {
SequenceKit::Standard(s) => s.serialize(serializer),
SequenceKit::Custom(items) => items.serialize(serializer),
}
}
}

#[derive(Deserialize, Serialize, Debug)]
pub struct Read {
read_id: String,
pub name: Option<String>,
Expand Down Expand Up @@ -229,25 +278,25 @@ impl Read {
let mut found_primer = false;

let result = if self.is_reverse() {
self.components(
self.get_read_span(
region.regions.as_ref().unwrap().iter().rev()
.skip_while(|region| {
let found = !(region.region_type.is_sequencing_primer() && region.region_id == self.primer_id);
let found = region.region_type.is_sequencing_primer() && region.region_id == self.primer_id;
if found {
found_primer = true;
}
found
!found
}).skip(1)
)
} else {
self.components(
self.get_read_span(
region.regions.as_ref().unwrap().iter()
.skip_while(|region| {
let found = !(region.region_type.is_sequencing_primer() && region.region_id == self.primer_id);
let found = region.region_type.is_sequencing_primer() && region.region_id == self.primer_id;
if found {
found_primer = true;
}
found
!found
}).skip(1)
)
};
Expand All @@ -259,7 +308,8 @@ impl Read {
}
}

fn components<'a, I: Iterator<Item = &'a Region>>(&self, regions: I) -> Vec<(&'a Region, Range<u32>)> {
/// Get the regions of the read.
fn get_read_span<'a, I: Iterator<Item = &'a Region>>(&self, regions: I) -> Vec<(&'a Region, Range<u32>)> {
let mut result = Vec::new();
let read_len = self.max_len;
let mut cur_pos = 0;
Expand Down Expand Up @@ -297,14 +347,14 @@ impl Read {
}
}

#[derive(Deserialize, Debug)]
#[derive(Deserialize, Serialize, Debug)]
#[serde(rename_all = "lowercase")]
pub enum Strand {
Pos,
Neg,
}

#[derive(Deserialize, Debug, Clone)]
#[derive(Deserialize, Serialize, Debug, Clone)]
pub struct File {
pub file_id: String,
pub filename: String,
Expand Down Expand Up @@ -336,7 +386,7 @@ impl File {
}
}

#[derive(Deserialize, Debug, Copy, Clone)]
#[derive(Deserialize, Serialize, Debug, Copy, Clone)]
#[serde(rename_all = "lowercase")]
pub enum UrlType {
Local,
Expand All @@ -345,7 +395,7 @@ pub enum UrlType {
Https,
}

#[derive(Deserialize, Debug, Clone)]
#[derive(Deserialize, Serialize, Debug, Clone)]
pub struct Region {
pub region_id: String,
pub region_type: RegionType,
Expand All @@ -364,7 +414,7 @@ impl Region {
}
}

#[derive(Deserialize, Debug, Copy, Clone, PartialEq)]
#[derive(Deserialize, Serialize, Debug, Copy, Clone, PartialEq)]
#[serde(rename_all = "lowercase")]
pub enum RegionType {
Barcode,
Expand Down Expand Up @@ -443,7 +493,7 @@ impl RegionType {
}
}

#[derive(Deserialize, Debug, Copy, Clone, PartialEq)]
#[derive(Deserialize, Serialize, Debug, Copy, Clone, PartialEq)]
#[serde(rename_all = "lowercase")]
pub enum SequenceType {
Fixed, // sequence string is known and fixed in length and nucleotide composition
Expand All @@ -452,7 +502,7 @@ pub enum SequenceType {
Joined, // the sequence is created from nested regions and the regions property must contain Regions
}

#[derive(Deserialize, Debug, Clone)]
#[derive(Deserialize, Serialize, Debug, Clone)]
pub struct Onlist {
pub file_id: String,
pub filename: String,
Expand All @@ -473,7 +523,7 @@ impl Onlist {
}
}

#[derive(Deserialize, Debug, Clone, Copy)]
#[derive(Deserialize, Serialize, Debug, Clone, Copy)]
#[serde(rename_all = "lowercase")]
pub enum Location {
Local,
Expand Down Expand Up @@ -503,8 +553,14 @@ mod tests {
let yaml_str = fs::read_to_string("tests/data/spec.yaml").expect("Failed to read file");

let assay: Assay = serde_yaml::from_str(&yaml_str).expect("Failed to parse YAML");
for x in assay.get_index_of(Modality::Protein) {
println!("{:?}", x);
for (read, regions) in assay.get_index_of(Modality::Rna) {
println!("{}: {:?}", read.read_id, regions.into_iter().map(|x| (x.0.region_type, x.1)).collect::<Vec<_>>());
}
for (read, regions) in assay.get_index_of(Modality::Atac) {
println!("{}: {:?}", read.read_id, regions.into_iter().map(|x| (x.0.region_type, x.1)).collect::<Vec<_>>());
}
for (read, regions) in assay.get_index_of(Modality::Protein) {
println!("{}: {:?}", read.read_id, regions.into_iter().map(|x| (x.0.region_type, x.1)).collect::<Vec<_>>());
}
}
}

0 comments on commit 1028fb0

Please sign in to comment.