Skip to content

Commit

Permalink
Start on updates based on accession
Browse files Browse the repository at this point in the history
  • Loading branch information
@Chris7
Chris7 committed Oct 16, 2024
1 parent 6e1d5ce commit bb5b0ee
Show file tree
Hide file tree
Showing 2 changed files with 81 additions and 29 deletions.
4 changes: 4 additions & 0 deletions src/models/path.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -156,6 +156,10 @@ impl Path {
paths
}

pub fn query(conn: &Connection, query: &str, placeholders: Vec<Value>) -> Vec<Path> {
Path::get_paths(conn, query, placeholders)
}

pub fn get_paths_for_collection(conn: &Connection, collection_name: &str) -> Vec<Path> {
let query = "SELECT * FROM path JOIN block_group ON path.block_group_id = block_group.id WHERE block_group.collection_name = ?1";
Path::get_paths(conn, query, vec![Value::from(collection_name.to_string())])
Expand Down
106 changes: 77 additions & 29 deletions src/updates/vcf.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ use noodles::vcf;
use noodles::vcf::variant::record::samples::series::value::genotype::Phasing;
use noodles::vcf::variant::record::samples::series::Value;
use noodles::vcf::variant::record::samples::Sample as NoodlesSample;
use noodles::vcf::variant::record::AlternateBases;
use noodles::vcf::variant::record::{AlternateBases, ReferenceBases};
use noodles::vcf::variant::Record;
use rusqlite::{session, types::Value as SQLValue, Connection};

Expand Down Expand Up @@ -51,12 +51,32 @@ impl<'a> BlockGroupCache<'_> {
if let Some(block_group_id) = block_group_lookup {
*block_group_id
} else {
let new_block_group_id = BlockGroup::get_or_create_sample_block_group(
block_group_cache.conn,
collection_name,
sample_name,
&name,
);
// see if a path exists already referencing this blockgroup. Reason is accessions
let mut placeholders: Vec<SQLValue> = vec![];
placeholders.push(name.clone().into());
placeholders.push(collection_name.to_string().into());
let mut bg_query = "bg.collection_name = ?2".to_string();
if sample_name.is_empty() {
bg_query.push_str(" AND bg.sample_name is null");
} else {
bg_query.push_str(" AND bg.sample_name = ?3");
placeholders.push(sample_name.to_string().into());
}

let mut new_block_group_id;

let paths = Path::query(block_group_cache.conn, &format!("select p.* from path p left join block_group bg on (p.block_group_id = bg.id) where p.name = ?1 AND {bg_query}"), placeholders.clone());
println!("p is {paths:?} {bg_query} {placeholders:?}");
if paths.len() == 1 {
new_block_group_id = paths.first().unwrap().block_group_id;
} else {
new_block_group_id = BlockGroup::get_or_create_sample_block_group(
block_group_cache.conn,
collection_name,
sample_name,
&name,
);
}
block_group_cache
.cache
.insert(block_group_key, new_block_group_id);
Expand Down Expand Up @@ -216,13 +236,8 @@ pub fn update_with_vcf(
let mut vcf_entries = vec![];

if !fixed_sample.is_empty() && !genotype.is_empty() {
let sample_bg_id = BlockGroupCache::lookup(
&mut block_group_cache,
collection_name,
&fixed_sample,
seq_name.clone(),
);
let sample_path = PathCache::lookup(&mut path_cache, sample_bg_id, seq_name.clone());
let mut sample_bg_id: Option<i64> = None;
let mut sample_path: Option<Path> = None;

for (chromosome_index, genotype) in genotype.iter().enumerate() {
if let Some(gt) = genotype {
Expand All @@ -232,10 +247,23 @@ pub fn update_with_vcf(
Phasing::Phased => 1,
Phasing::Unphased => 0,
};
if sample_bg_id.is_none() {
sample_bg_id = Some(BlockGroupCache::lookup(
&mut block_group_cache,
collection_name,
&fixed_sample,
seq_name.clone(),
));
sample_path = Some(PathCache::lookup(
&mut path_cache,
sample_bg_id.unwrap(),
seq_name.clone(),
));
}
vcf_entries.push(VcfEntry {
ids: record.ids().as_ref().to_string(),
block_group_id: sample_bg_id,
path: sample_path.clone(),
block_group_id: sample_bg_id.unwrap(),
path: sample_path.clone().unwrap(),
sample_name: fixed_sample.clone(),
alt_seq,
chromosome_index: chromosome_index as i64,
Expand All @@ -246,15 +274,8 @@ pub fn update_with_vcf(
}
} else {
for (sample_index, sample) in record.samples().iter().enumerate() {
let sample_bg_id = BlockGroupCache::lookup(
&mut block_group_cache,
collection_name,
&sample_names[sample_index],
seq_name.clone(),
);
let sample_path =
PathCache::lookup(&mut path_cache, sample_bg_id, seq_name.clone());

let mut sample_bg_id: Option<i64> = None;
let mut sample_path: Option<Path> = None;
let genotype = sample.get(&header, "GT");
if genotype.is_some() {
if let Value::Genotype(genotypes) = genotype.unwrap().unwrap().unwrap() {
Expand All @@ -266,12 +287,25 @@ pub fn update_with_vcf(
Phasing::Unphased => 0,
};
if let Some(allele) = allele {
if sample_bg_id.is_none() {
sample_bg_id = Some(BlockGroupCache::lookup(
&mut block_group_cache,
collection_name,
&sample_names[sample_index],
seq_name.clone(),
));
sample_path = Some(PathCache::lookup(
&mut path_cache,
sample_bg_id.unwrap(),
seq_name.clone(),
));
}
if allele != 0 {
let alt_seq = alt_alleles[allele - 1];
vcf_entries.push(VcfEntry {
ids: record.ids().as_ref().to_string(),
block_group_id: sample_bg_id,
path: sample_path.clone(),
block_group_id: sample_bg_id.unwrap(),
path: sample_path.clone().unwrap(),
sample_name: sample_names[sample_index].clone(),
alt_seq,
chromosome_index: chromosome_index as i64,
Expand All @@ -295,8 +329,10 @@ pub fn update_with_vcf(
SequenceCache::lookup(&mut sequence_cache, "DNA", vcf_entry.alt_seq.to_string());
let sequence_string = sequence.get_sequence(None, None);

println!("with {vcf_entry:?}");

let parent_path_id : i64 = *parent_block_groups.entry((collection_name, vcf_entry.path.id)).or_insert_with(|| {
let parent_bg = &BlockGroup::query(conn, "select * from block_group where collection_name = ?1 AND sample_name is null and name = ?2", vec![SQLValue::from(collection_name.to_string()), SQLValue::from(vcf_entry.path.name.clone())])[0];
let parent_bg = &Path::query(conn, "select * from path p left join block_group bg on (p.block_group_id = bg.id) where bg.collection_name = ?1 AND sample_name is null and name = ?2", vec![SQLValue::from(collection_name.to_string()), SQLValue::from(vcf_entry.path.name.clone())])[0];
let parent_path =
PathCache::lookup(&mut path_cache, parent_bg.id, vcf_entry.path.name.clone());
parent_path.id
Expand Down Expand Up @@ -688,7 +724,7 @@ mod tests {
vcf_path.push("fixtures/accession.vcf");
let mut fasta_path = PathBuf::from(env!("CARGO_MANIFEST_DIR"));
fasta_path.push("fixtures/simple.fa");
let conn = &get_connection(None);
let conn = &get_connection("t2.db");
let db_uuid = metadata::get_db_uuid(conn);
let op_conn = &get_operation_connection(None);
setup_db(op_conn, &db_uuid);
Expand Down Expand Up @@ -721,5 +757,17 @@ mod tests {
.len(),
1
);

let mut vcf_path = PathBuf::from(env!("CARGO_MANIFEST_DIR"));
vcf_path.push("fixtures/accession_2.vcf");

update_with_vcf(
&vcf_path.to_str().unwrap().to_string(),
&collection,
"".to_string(),
"".to_string(),
conn,
op_conn,
);
}
}

0 comments on commit bb5b0ee

Please sign in to comment.