Merge pull request #4 from aertslab/development

v0.1.1

CHANGELOG.md

@@ -0,0 +1,7 @@
+# Changelog
+
+## v0.1.1
+
+### Added
+
+- **[004a265](https://github.com/aertslab/scatac_fragment_tools/commit/004a2654ecd5ed0a33be78f6fa5789c0a41deafb)**: Allow barcodes to map to multiple cell types while splitting fragments by cell type.

pyproject.toml

@@ -29,7 +29,7 @@ dependencies = [
 homepage = "https://github.com/aertslab/scatac_fragment_tools/"
 documentation = "https://aertslab.github.io/scatac_fragment_tools/"
 repository = "https://github.com/aertslab/scatac_fragment_tools/"
-changelog = "https://github.com/aertslab/scatac_fragment_tools/commits/main/"
+changelog = "https://raw.githubusercontent.com/aertslab/scatac_fragment_tools/CHANGELOG.md"
 
 [project.optional-dependencies]
 development = [

rust/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "_rust_scatac_fragment_tools"
-version = "0.1.0"
+version = "0.1.1"
 authors = ["Seppe De Winter <[email protected]>", "Gert Hulselmans <[email protected]>"]
 edition = "2021"
 

rust/src/lib.rs

@@ -44,10 +44,13 @@ fn split_fragments_by_cell_barcode(
     verbose: bool,
 ) -> PyResult<()> {
     // Invert cell_type_to_cell_barcodes
-    let mut cell_barcode_to_cell_type: HashMap<String, String> = HashMap::new();
+    let mut cell_barcode_to_cell_type: HashMap<String, Vec<String>> = HashMap::new();
     for (cell_type, cell_barcodes) in cell_type_to_cell_barcodes.iter() {
         for cell_barcode in cell_barcodes.iter() {
-            cell_barcode_to_cell_type.insert(cell_barcode.to_string(), cell_type.to_string());
+            cell_barcode_to_cell_type
+                .entry(cell_barcode.to_string())
+                .or_insert(Vec::new())
+                .push(cell_type.to_string());
         }
     }
     split_fragments::split_fragments_by_cell_barcode(

rust/src/split_fragments.rs

@@ -83,7 +83,7 @@ fn sanitize_string_for_filename(s: String) -> String {
 pub fn split_fragments_by_cell_barcode(
     path_to_fragments: &String,
     path_to_output_folder: &String,
-    cell_barcode_to_cell_type: HashMap<String, String>,
+    cell_barcode_to_cell_type: HashMap<String, Vec<String>>,
     chromsizes: HashMap<String, u64>,
     number_of_threads: u32,
     verbose: bool,
@@ -101,7 +101,11 @@ pub fn split_fragments_by_cell_barcode(
         )
     });
     let mut cell_type_to_writer: HashMap<&String, LazyBgzfWriter> = HashMap::new();
-    let unique_cell_types: Vec<&String> = cell_barcode_to_cell_type.values().unique().collect();
+    let unique_cell_types: Vec<&String> = cell_barcode_to_cell_type
+        .values()
+        .flatten()
+        .unique()
+        .collect();
     for cell_type in unique_cell_types {
         let cell_type_name = sanitize_string_for_filename(cell_type.clone().to_string());
         let path_to_output = format!(
@@ -145,10 +149,12 @@ pub fn split_fragments_by_cell_barcode(
         // loop over reads
         while not_at_end {
             let read_cb = read_as_str.split('\t').nth(3).unwrap().to_string();
-            if let Some(cell_type) = cell_barcode_to_cell_type.get(&read_cb) {
-                let writer = cell_type_to_writer.get_mut(cell_type).unwrap();
-                writer.write(&read).unwrap();
-                writer.write(b"\n").unwrap();
+            if let Some(cell_types) = cell_barcode_to_cell_type.get(&read_cb) {
+                for cell_type in cell_types {
+                    let writer = cell_type_to_writer.get_mut(cell_type).unwrap();
+                    writer.write(&read).unwrap();
+                    writer.write(b"\n").unwrap();
+                }
             }
             read.clear();
             not_at_end = tbx_reader.read(&mut read).unwrap();

tests/split/cell_type_annotation.tsv

@@ -1,6 +1,5 @@
 sample	cell_type	cell_barcode
 A	type_1	TTAGCTTAGGAGAACA-1
-A	type_1	TTAGCTTAGGAGAACA-1
 A	type_1	ATATTCCTCTTGTACT-1
 A	type_2	TGTGACAGTACAACGG-1
 A	type_2	CATGCCTTCTCTGACC-1

tests/split/cell_type_annotation_one_bc_multiple_types.tsv

@@ -0,0 +1,30 @@
+sample	cell_type	cell_barcode
+A	type_1	TTAGCTTAGGAGAACA-1
+A	type_1	ATATTCCTCTTGTACT-1
+A	type_2	TTAGCTTAGGAGAACA-1
+A	type_2	CATGCCTTCTCTGACC-1
+A	type_2	ATCGAGTAGGTTCGAG-1
+A	type_3	CTCTCAGGTCCCTTTG-1
+A	type_3	TTCGGTCTCACGTGTA-1
+A	type_3	GTGACATCATTGTTCT-1
+A	type_4	AAGGAGCCATCGACCG-1
+A	type_4	ACCAAACTCTTAAGCG-1
+A	type_4	CATTGGATCTCTTCCT-1
+A	type_5	AGGCGAAAGGTCTTTG-1
+A	type_5	AACGAGGCATCATGTG-1
+A	type_5	CTACTTAGTCATGAGG-1
+B	type_1	ATTACCTGTGTGCTTA-1
+B	type_1	CATAACGTCGGTTGTA-1
+B	type_1	ATGTCTTTCGGTCCGA-1
+B	type_2	CAATCCCGTAGCGTTT-1
+B	type_2	GCCATAATCATCGCTC-1
+B	type_2	CAACGTAAGGCAAGGG-1
+B	type_3	TATCGAGGTTGCCGCA-1
+B	type_3	CATTCCGAGCTAACAA-1
+B	type_3	CCTCCCTGTAAAGCTA-1
+B	type_4	CAAGCTACACGTTGTA-1
+B	type_4	CTGCTCATCACAAGCT-1
+B	type_4	CAGTATGGTTCTTTGT-1
+B	type_5	TTGCACCCATTAGCAC-1
+B	type_5	CAGCCTTCATCTCTCG-1
+B	type_5	TTGCGGGTCGTCAACA-1

tests/split/test_split.py

@@ -6,48 +6,77 @@
 
 TEST_DIRECTORY = pathlib.Path(__file__).parent.absolute()
 
+FILES_ALL_BARCODES_MAPPING_TO_SINGLE_TYPE = {
+    "a.fragments": "a.fragments.tsv.gz",
+    "a.fragment_index": "a.fragments.tsv.gz.tbi",
+    "b.fragments": "b.fragments.tsv.gz",
+    "b.fragment_index": "b.fragments.tsv.gz.tbi",
+    "sample_to_fragment": "sample_to_fragment.tsv",
+    "cell_type_annotation": "cell_type_annotation.tsv",
+    "chrom_sizes": "hg38.chrom.sizes"
+}
+
+FILES_SOME_BARCODES_MAPPING_TO_MULTIPLE_TYPES = {
+    "a.fragments": "a.fragments.tsv.gz",
+    "a.fragment_index": "a.fragments.tsv.gz.tbi",
+    "b.fragments": "b.fragments.tsv.gz",
+    "b.fragment_index": "b.fragments.tsv.gz.tbi",
+    "sample_to_fragment": "sample_to_fragment.tsv",
+    "cell_type_annotation": "cell_type_annotation_one_bc_multiple_types.tsv",
+    "chrom_sizes": "hg38.chrom.sizes"
+}
+
 def test_entrypoint():
     exit_status = os.system("scatac_fragment_tools split")
     assert exit_status == 0
 
-def run_split_command(tmp_path, output_folder):
-    os.system(f"cp {TEST_DIRECTORY}/a.fragments.tsv.gz {tmp_path}")
-    os.system(f"cp {TEST_DIRECTORY}/a.fragments.tsv.gz.tbi {tmp_path}")
-    os.system(f"cp {TEST_DIRECTORY}/b.fragments.tsv.gz {tmp_path}")
-    os.system(f"cp {TEST_DIRECTORY}/b.fragments.tsv.gz.tbi {tmp_path}")
-    os.system(f"cp {TEST_DIRECTORY}/sample_to_fragment.tsv {tmp_path}")
-    os.system(f"cp {TEST_DIRECTORY}/cell_type_annotation.tsv {tmp_path}")
-    os.system(f"cp {TEST_DIRECTORY}/hg38.chrom.sizes {tmp_path}")
+def run_split_command(tmp_path, output_folder, file_dict):
+    path_to_a_fragments = os.path.join(TEST_DIRECTORY, file_dict["a.fragments"])
+    path_to_a_fragment_index = os.path.join(TEST_DIRECTORY, file_dict["a.fragment_index"])
+    path_to_b_fragments = os.path.join(TEST_DIRECTORY, file_dict["b.fragments"])
+    path_to_b_fragment_index = os.path.join(TEST_DIRECTORY, file_dict["b.fragment_index"])
+    path_to_sample_to_fragment = os.path.join(TEST_DIRECTORY, file_dict["sample_to_fragment"])
+    path_to_cell_type_annotation = os.path.join(TEST_DIRECTORY, file_dict["cell_type_annotation"])
+    path_to_chrom_sizes = os.path.join(TEST_DIRECTORY, file_dict["chrom_sizes"])
+    os.system(f"cp {path_to_a_fragments} {tmp_path}")
+    os.system(f"cp {path_to_a_fragment_index} {tmp_path}")
+    os.system(f"cp {path_to_b_fragments} {tmp_path}")
+    os.system(f"cp {path_to_b_fragment_index} {tmp_path}")
+    os.system(f"cp {path_to_sample_to_fragment} {tmp_path}")
+    os.system(f"cp {path_to_cell_type_annotation} {tmp_path}")
+    os.system(f"cp {path_to_chrom_sizes} {tmp_path}")
+
     COMMAND = f"""cd {tmp_path} && \
     scatac_fragment_tools split \
-        -f {tmp_path}/sample_to_fragment.tsv \
-        -b {tmp_path}/cell_type_annotation.tsv \
-        -c {tmp_path}/hg38.chrom.sizes \
+        -f {path_to_sample_to_fragment} \
+        -b {path_to_cell_type_annotation} \
+        -c {path_to_chrom_sizes} \
         -o {output_folder} \
         -t {tmp_path} \
     """
     return os.system(COMMAND)
 
-def test_split_command(tmp_path):
+def split_command_test_helper(tmp_path, file_dict):
     output_folder = os.path.join(tmp_path, "output")
     os.makedirs(output_folder, exist_ok=True)
-    exit_status = run_split_command(tmp_path, output_folder)
+    exit_status = run_split_command(tmp_path, output_folder, file_dict)
     assert exit_status == 0
 
     a_fragments = pl.read_csv(
-        TEST_DIRECTORY.joinpath("a.fragments.tsv.gz"),
+        TEST_DIRECTORY.joinpath(file_dict["a.fragments"]),
         separator = "\t",
         has_header = False
     )
     b_fragments = pl.read_csv(
-        TEST_DIRECTORY.joinpath("b.fragments.tsv.gz"),
+        TEST_DIRECTORY.joinpath(file_dict["b.fragments"]),
         separator = "\t",
         has_header = False
     )
     cell_annotations = pl.read_csv(
-        TEST_DIRECTORY.joinpath("cell_type_annotation.tsv"),
+        TEST_DIRECTORY.joinpath(file_dict["cell_type_annotation"]),
         separator = "\t"
     )
+
     for row in cell_annotations \
             .select(pl.col("cell_type")) \
             .unique() \
@@ -72,3 +101,10 @@ def test_split_command(tmp_path):
             generated_fragments_cell_type
         )
 
+
+def test_split_command_bc_single_type(tmp_path):
+    split_command_test_helper(tmp_path, FILES_ALL_BARCODES_MAPPING_TO_SINGLE_TYPE)
+
+def test_split_command_barcode_mapping_multiple_types(tmp_path):
+    split_command_test_helper(tmp_path, FILES_SOME_BARCODES_MAPPING_TO_MULTIPLE_TYPES)
+