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Merge pull request #5 from ginkgobioworks/cleanup
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Cleanup
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@Chris7
Chris7 committed Jul 24, 2024
2 parents a210525 + 0c9c1e4 commit e31527d
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Showing 4 changed files with 422 additions and 289 deletions.
3 changes: 2 additions & 1 deletion migrations/01-initial/up.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ CREATE TABLE sample (
CREATE TABLE sequence (
hash TEXT PRIMARY KEY NOT NULL,
sequence_type TEXT NOT NULL,
sequence TEXT NOT NULL,
sequence TEXT,
"length" INTEGER NOT NULL
);

Expand All @@ -35,6 +35,7 @@ CREATE TABLE block (
FOREIGN KEY(path_id) REFERENCES path(id),
constraint chk_strand check (strand in ('-1', '1', '0', '.', '?'))
);
CREATE UNIQUE INDEX block_uidx ON block(sequence_hash, path_id, start, end, strand);

CREATE TABLE edges (
id INTEGER PRIMARY KEY NOT NULL,
Expand Down
77 changes: 0 additions & 77 deletions src/lib.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -35,83 +35,6 @@ mod tests {
conn
}

// #[test]
// fn create_node() {
// let mut conn = get_connection();
// let node = models::Node::create(&mut conn, "A".to_string());
// assert_eq!(node.base, "A");
// }
//
// #[test]
// fn create_nodes() {
// let mut conn = get_connection();
// let nodes = models::Node::bulk_create(&mut conn, &vec!["A".to_string(), "T".to_string()]);
// assert_eq!(nodes[0].base, "A");
// assert_eq!(nodes[1].base, "T");
// }
//
// #[test]
// fn create_edge() {
// let mut conn = get_connection();
// let node = models::Node::create(&mut conn, "A".to_string());
// let node2 = models::Node::create(&mut conn, "T".to_string());
// let edge = models::Edge::create(&mut conn, node.id, node2.id);
// assert_eq!(edge.source_id, node.id);
// assert_eq!(edge.target_id, node2.id);
// }
//
// #[test]
// fn create_edges() {
// let mut conn = get_connection();
// let node = models::Node::create(&mut conn, "A".to_string());
// let node2 = models::Node::create(&mut conn, "T".to_string());
// let node3 = models::Node::create(&mut conn, "C".to_string());
// let edges = models::Edge::bulk_create(&mut conn, &vec![models::Edge{id: 0, source_id: node.id, target_id: node2.id}, models::Edge{id: 0, source_id: node2.id, target_id: node3.id}]);
// assert_eq!(edges[0].source_id, node.id);
// assert_eq!(edges[0].target_id, node2.id);
// assert_eq!(edges[1].source_id, node2.id);
// assert_eq!(edges[1].target_id, node3.id);
// }
//
// #[test]
// fn create_genome() {
// let mut conn = get_connection();
// let obj = models::Genome::create(&mut conn, "hg19".to_string());
// assert_eq!(obj.name, "hg19");
// }
//
// #[test]
// fn create_genomes() {
// let mut conn = get_connection();
// let objs = models::Genome::bulk_create(&mut conn, &vec!["hg19".to_string(), "mm9".to_string()]);
// assert_eq!(objs[0].name, "hg19");
// assert_eq!(objs[1].name, "mm9");
// }
//
// #[test]
// fn create_contig() {
// let mut conn = get_connection();
// let genome = models::Genome::create(&mut conn, String::from("hg19"));
// let obj_id = models::GenomeContig::create(&mut conn, genome.id, String::from("chr1"), &String::from("atcg"), false);
// let contig = models::GenomeContig::get(&mut conn, obj_id);
// assert_eq!(contig.name, "chr1");
// }
//
// #[test]
// fn create_genome_fragment() {
// let mut conn = get_connection();
// let obj = models::Genome::create(&mut conn, "hg19".to_string());
// assert_eq!(obj.name, "hg19");
// }
//
// #[test]
// fn create_genome_fragments() {
// let mut conn = get_connection();
// let objs = models::Genome::bulk_create(&mut conn, &vec!["hg19".to_string(), "mm9".to_string()]);
// assert_eq!(objs[0].name, "hg19");
// assert_eq!(objs[1].name, "mm9");
// }

#[test]
fn it_hashes() {
assert_eq!(
Expand Down
77 changes: 53 additions & 24 deletions src/main.rs
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Original file line number Diff line number Diff line change
@@ -1,15 +1,17 @@
#![allow(warnings)]
use clap::{Parser, Subcommand};
use std::collections::HashSet;
use std::fmt::Debug;
use std::path::PathBuf;

use bio::io::fasta;
use gen::get_connection;
use gen::migrations::run_migrations;
use gen::models::{self};
use gen::models::{self, Block, Path};
use noodles::vcf;
use noodles::vcf::variant::record::samples::series::Value;
use noodles::vcf::variant::record::samples::{Sample, Series};
use noodles::vcf::variant::record::{AlternateBases, Samples};
use noodles::vcf::variant::record::{AlternateBases, ReferenceBases, Samples};
use noodles::vcf::variant::Record;
use rusqlite::Connection;
use std::io;
Expand All @@ -34,6 +36,9 @@ enum Commands {
/// The path to the database you wish to utilize
#[arg(short, long)]
db: String,
/// Don't store the sequence in the database, instead store the filename
#[arg(short, long, action)]
shallow: bool,
},
/// Update a sequence collection with new data
Update {
Expand All @@ -52,7 +57,7 @@ enum Commands {
},
}

fn import_fasta(fasta: &String, name: &String, conn: &mut Connection) {
fn import_fasta(fasta: &String, name: &String, shallow: bool, conn: &mut Connection) {
let mut reader = fasta::Reader::from_file(fasta).unwrap();

run_migrations(conn);
Expand All @@ -63,16 +68,16 @@ fn import_fasta(fasta: &String, name: &String, conn: &mut Connection) {
for result in reader.records() {
let record = result.expect("Error during fasta record parsing");
let sequence = String::from_utf8(record.seq().to_vec()).unwrap();
let seq_hash = models::Sequence::create(conn, "DNA".to_string(), &sequence);
let seq_hash = models::Sequence::create(conn, "DNA".to_string(), &sequence, !shallow);
let path =
models::Path::create(conn, &collection.name, None, &record.id().to_string(), None);
let block = models::Block::create(
let block = Block::create(
conn,
&seq_hash,
path.id,
0,
(sequence.len() as i32),
"1".to_string(),
&"1".to_string(),
);
let edge = models::Edge::create(conn, block.id, None);
}
Expand All @@ -82,7 +87,7 @@ fn import_fasta(fasta: &String, name: &String, conn: &mut Connection) {
}
}

fn update_with_vcf(vcf_path: &String, name: &String, conn: &mut Connection) {
fn update_with_vcf(vcf_path: &String, collection_name: &String, conn: &mut Connection) {
run_migrations(conn);

let mut reader = vcf::io::reader::Builder::default()
Expand All @@ -97,42 +102,53 @@ fn update_with_vcf(vcf_path: &String, name: &String, conn: &mut Connection) {
let record = result.unwrap();
let seq_name = record.reference_sequence_name().to_string();
let ref_allele = record.reference_bases();
// this converts the coordinates to be zero based, start inclusive, end exclusive
let ref_start = record.variant_start().unwrap().unwrap().get() - 1;
let ref_end = record.variant_end(&header).unwrap().get() - 1;
let ref_end = record.variant_end(&header).unwrap().get();
let alt_bases = record.alternate_bases();
let alt_alleles: Vec<_> = alt_bases.iter().collect::<io::Result<_>>().unwrap();
for (sample_index, sample) in record.samples().iter().enumerate() {
let genotype = sample.get(&header, "GT");
let mut seen_haplotypes: HashSet<i32> = HashSet::new();
if genotype.is_some() {
if let Value::Genotype(genotypes) = genotype.unwrap().unwrap().unwrap() {
for gt in genotypes.iter() {
if gt.is_ok() {
let (haplotype, phasing) = gt.unwrap();
let haplotype = haplotype.unwrap();
if haplotype != 0 {
if haplotype != 0 && !seen_haplotypes.contains(&(haplotype as i32)) {
let alt_seq = alt_alleles[haplotype - 1];
// TODO: new sequence may not be real and be <DEL> or some sort. Handle these.
let new_sequence_hash = models::Sequence::create(
conn,
"DNA".to_string(),
&alt_seq.to_string(),
true,
);
let (parent_path_id, haplotype_path_id) =
models::Path::get_or_create_sample_path(
conn,
name,
&sample_names[sample_index],
&seq_name,
haplotype as i32,
);
models::Path::insert_change(
let sample_path_id = models::Path::get_or_create_sample_path(
conn,
haplotype_path_id,
collection_name,
&sample_names[sample_index],
&seq_name,
haplotype as i32,
);
let new_block_id = Block::create(
conn,
&new_sequence_hash,
sample_path_id,
0,
alt_seq.len() as i32,
&"1".to_string(),
);
Path::insert_change(
conn,
sample_path_id,
ref_start as i32,
ref_end as i32,
&new_sequence_hash,
new_block_id.id,
);
}
seen_haplotypes.insert(haplotype as i32);
}
}
}
Expand All @@ -145,9 +161,12 @@ fn main() {
let cli = Cli::parse();

match &cli.command {
Some(Commands::Import { fasta, name, db }) => {
import_fasta(fasta, name, &mut get_connection(db))
}
Some(Commands::Import {
fasta,
name,
db,
shallow,
}) => import_fasta(fasta, name, *shallow, &mut get_connection(db)),
Some(Commands::Update {
name,
db,
Expand Down Expand Up @@ -180,6 +199,7 @@ mod tests {
import_fasta(
&fasta_path.to_str().unwrap().to_string(),
&"test".to_string(),
false,
&mut get_connection(),
);
}
Expand All @@ -192,7 +212,16 @@ mod tests {
fasta_path.push("fixtures/simple.fa");
let conn = &mut get_connection();
let collection = "test".to_string();
import_fasta(&fasta_path.to_str().unwrap().to_string(), &collection, conn);
import_fasta(
&fasta_path.to_str().unwrap().to_string(),
&collection,
false,
conn,
);
update_with_vcf(&vcf_path.to_str().unwrap().to_string(), &collection, conn);
assert_eq!(
Path::sequence(conn, &collection, Some(&"foo".to_string()), "m123", 1),
"ATCATCGATCGATCGATCGGGAACACACAGAGA"
);
}
}
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