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Working version! More info obtained than Star!
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@stela2502
stela2502 committed Feb 23, 2024
1 parent 8f41ff3 commit 5bf2134
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Showing 14 changed files with 1,674,244 additions and 33,690 deletions.
3 changes: 2 additions & 1 deletion src/analysis.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -882,7 +882,8 @@ impl Analysis{
results.stop_file_io_time();

println!("filtering cells");
self.gex.mtx_counts( &mut self.genes, &self.gene_names, min_umi, self.gex.num_threads ) ;
self.gex.update_genes_to_print( &self.genes, &self.gene_names );
self.gex.mtx_counts( &mut self.genes, min_umi, self.gex.num_threads ) ;

results.stop_multi_processor_time();
println!("writing gene expression");
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3 changes: 2 additions & 1 deletion src/analysis_te.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -819,7 +819,8 @@ impl AnalysisTE{
results.stop_file_io_time();

println!("filtering cells");
self.gex.mtx_counts( &mut self.te_index_obj, &self.te_names, min_umi, self.gex.num_threads ) ;
self.gex.update_genes_to_print( &self.te_index_obj, &self.te_names );
self.gex.mtx_counts( &mut self.te_index_obj, min_umi, self.gex.num_threads ) ;

results.stop_multi_processor_time();
println!("writing expression sets:");
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2 changes: 1 addition & 1 deletion src/fast_mapper/fast_mapper.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -959,7 +959,7 @@ impl FastMapper{
//println!( "Pushing {} -> {}", obj, *id-1);
ret.push( name.to_string() ) ;
}
ret.push("AsignedSampleName".to_string());
ret.push("AssignedSampleName".to_string());
ret.push("FractionTotal".to_string());
ret.push("n".to_string());
ret.push("dist to nr.2 [%max]".to_string());
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59 changes: 33 additions & 26 deletions src/singlecelldata/singlecelldata.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@ pub struct SingleCellData{
//kmer_size: usize,
//kmers: BTreeMap<u64, u32>,
data: [BTreeMap< u64, CellData>; u8::MAX as usize],
genes_to_print: Vec::<String>,
//ambient_cell_content: BTreeMap< u64, CellData>,
checked: bool,
passing: usize,
Expand Down Expand Up @@ -63,6 +64,7 @@ impl SingleCellData{
Self {
//kmer_size,
data,
genes_to_print: Vec::<String>::with_capacity(4),
//ambient_cell_content: BTreeMap::new(),
checked,
passing,
Expand Down Expand Up @@ -193,7 +195,8 @@ impl SingleCellData{
let mut passed = 0;

if ! self.checked{
self.mtx_counts( genes, names, min_count, self.num_threads );
self.update_genes_to_print( genes, names);
self.mtx_counts( genes, min_count, self.num_threads );
}

//println!("We are here exporting a samples table and want these samples to be included: {:?}", names );
Expand Down Expand Up @@ -229,7 +232,9 @@ impl SingleCellData{

let rs = Path::new( &file_path ).exists();

if names.is_empty(){
self.update_genes_to_print( genes, names);

if self.genes_to_print.is_empty(){
eprintln!("No genes to report on - no data written to path {:?}", file_path.to_str());
return Ok(())
}
Expand Down Expand Up @@ -270,7 +275,7 @@ impl SingleCellData{
let file2 = GzEncoder::new(file_b, Compression::default());
let mut writer_b = BufWriter::with_capacity(4096,file2);
match writeln!( writer, "%%MatrixMarket matrix coordinate integer general\n{}",
self.mtx_counts( genes, names, min_count, self.num_threads ) ){
self.mtx_counts( genes, min_count, self.num_threads ) ){
Ok(_) => (),
Err(err) => {
eprintln!("write error: {err}");
Expand All @@ -289,7 +294,7 @@ impl SingleCellData{
let file3 = GzEncoder::new(file_f, Compression::default());
let mut writer_f = BufWriter::with_capacity(4096,file3);

for name in genes.names4sparse.keys() {
for name in &self.genes_to_print {
match writeln!( writer_f, "{name}\t{name}\tGene Expression" ){
Ok(_) => (),
Err(err) => {
Expand All @@ -304,15 +309,15 @@ impl SingleCellData{
let mut entries = 0;
let mut cell_id = 0;

let gene_ids = genes.ids_for_gene_names( names );
let gene_ids = genes.ids_for_gene_names( &self.genes_to_print );

for cell_obj in self.values() {
if ! cell_obj.passing {
continue;
}
cell_id += 1;

match writeln!( writer_b, "{}",cell_obj.name ){
match writeln!( writer_b, "Cell{}",cell_obj.name ){
Ok(_) => (),
Err(err) => {
eprintln!("write error: {err}");
Expand All @@ -338,15 +343,12 @@ impl SingleCellData{
Ok( () )
}
/// Update the gene names for export to sparse
pub fn update_names_4_sparse( &mut self, genes: &mut FastMapper, names:&Vec<String>) -> [usize; 2] {
/// returns the count of cells and the count of total gene values
pub fn update_genes_to_print( &mut self, genes: &FastMapper, names:&Vec<String>) -> [usize; 2] {

let mut entries = 0;
let _ncell = 0;
if ! self.checked{
panic!("Please always run mtx_counts before update_names_4_sparse");
}
genes.names4sparse.clear();
genes.max_id = 0; // reset to collect the passing genes

self.genes_to_print.clear();

let cell_keys:Vec<u64> = self.keys();
let chunk_size = cell_keys.len() / self.num_threads +1;
Expand All @@ -361,6 +363,10 @@ impl SingleCellData{
let gene_ids = genes.ids_for_gene_names( names );
for key in chunk {
if let Some(cell_obj) = self.get(key){
if self.checked & ! cell_obj.passing{
println!("ignoring cell");
continue;
}
for (id, int_id) in gene_ids.iter().enumerate() {
//for name in names {
n = *cell_obj.total_reads.get( &int_id ).unwrap_or(&0);
Expand All @@ -377,18 +383,19 @@ impl SingleCellData{
}).collect();

// Merge gene data from different chunks
let mut names4sparse = HashSet::<String>::new();

for (genelist, n) in &gene_data{
entries += n;
for name in genelist.keys() {
if ! genes.names4sparse.contains_key ( name ){
// Insert gene names into the FastMapper
genes.max_id +=1;
genes.names4sparse.insert( name.to_string() , genes.max_id );
}
names4sparse.insert( name.to_string() );
}
}

if genes.max_id ==0 && ! names.is_empty() {
self.genes_to_print = names4sparse.iter().cloned().collect();


/*if genes.max_id ==0 && ! names.is_empty() {
let mut to = 10;
if names.len() < 10{
to = names.len() -1;
Expand All @@ -403,12 +410,12 @@ impl SingleCellData{
used.push(name.to_string());
}
return self.update_names_4_sparse(genes, &used );
}
}*/
[ self.len(), entries ]
}


pub fn mtx_counts(&mut self, genes: &mut FastMapper, names: &Vec<String>, min_count:usize, num_threads: usize ) -> String{
pub fn mtx_counts(&mut self, genes: &mut FastMapper, min_count:usize, num_threads: usize ) -> String{


if ! self.checked{
Expand All @@ -434,7 +441,7 @@ impl SingleCellData{
let mut ret= Vec::<(u64, bool)>::with_capacity(chunk_size);
for key in chunk {
if let Some(cell_obj) = &self.get(key) {
let n = cell_obj.n_umi( genes, names );
let n = cell_obj.n_umi( genes, &self.genes_to_print );
ret.push( (key.clone(), n >= min_count) );
}
}
Expand All @@ -461,19 +468,19 @@ impl SingleCellData{

}

let ncell_and_entries = self.update_names_4_sparse( genes, names );
let ncell_and_entries = self.update_genes_to_print( &genes, &self.genes_to_print.clone() );
self.passing = ncell_and_entries[0];

let ret = format!("{} {} {}", genes.names4sparse.len(), ncell_and_entries[0], ncell_and_entries[1] );
let ret = format!("{} {} {}", self.genes_to_print.len(), ncell_and_entries[0], ncell_and_entries[1] );
//println!("mtx_counts -> final return: mtx_counts: {}", ret );
ret
}

pub fn n_reads( &mut self, genes: &mut FastMapper, names: &Vec<String> ) -> usize {
pub fn n_reads( &mut self, genes: &FastMapper, names: &Vec<String> ) -> usize {
let mut count = 0;

for cell_obj in self.values() {
count += cell_obj.n_reads( genes, names )
count += cell_obj.n_reads( &genes, names )
}
count
}
Expand Down
1 change: 1 addition & 0 deletions testData/.gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -10,3 +10,4 @@ cells*
/test_index/
/TEmapperTest/
/mapperTest/
Cell_IDs*
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