From 17d0af7c9e07dc60b64debcac0891709da4a3b44 Mon Sep 17 00:00:00 2001 From: Malte Benedikt Kuehl Date: Sat, 14 Sep 2024 13:59:58 +0200 Subject: [PATCH] Add piscem test file and improve unit test coverage --- pyproject.toml | 4 +- pytximport/core/_tximport.py | 15 +- pytximport/importers/_read_salmon.py | 11 - test/conftest.py | 27 +- test/data/piscem/res.quant | 15 + test/data/salmon/quant.sf.gz | Bin 0 -> 355 bytes test/data/transcript_name_mapping_human.tsv | 278221 +++++++++++++++++ test/test_piscem.py | 38 + test/test_salmon.py | 26 + test/test_transcript_gene_map.py | 29 +- test/test_transcript_level.py | 20 +- 11 files changed, 278370 insertions(+), 36 deletions(-) create mode 100644 test/data/piscem/res.quant create mode 100644 test/data/salmon/quant.sf.gz create mode 100644 test/data/transcript_name_mapping_human.tsv create mode 100644 test/test_piscem.py diff --git a/pyproject.toml b/pyproject.toml index e658f01..a4e9937 100755 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "flit_core.buildapi" [project] name = "pytximport" -description = "A python implementation of tximport to transform transcript into gene counts" +description = "A python implementation of `tximport` to transform transcript into gene counts" requires-python = ">=3.9" license = { file = "LICENSE" } authors = [{ name = "Malte Kuehl", email = "malte.kuehl@clin.au.dk" }] @@ -25,7 +25,7 @@ classifiers = [ ] dynamic = ["version"] dependencies = [ - "anndata>=0.9.0", + "anndata>=0.8.0", "click>=8.0.0,<9", "flox>=0.9.0,<0.10.0", "h5py>=3.0.0,<4", diff --git a/pytximport/core/_tximport.py b/pytximport/core/_tximport.py index 9c99a8a..dc4fa76 100644 --- a/pytximport/core/_tximport.py +++ b/pytximport/core/_tximport.py @@ -199,9 +199,18 @@ def tximport( importer = read_tsv elif data_type == "piscem": - id_column = "Name" if id_column is None else id_column - counts_column = "NumReads" if counts_column is None else counts_column - length_column = "EffectiveLength" if length_column is None else length_column + warning( + ( + "Assuming a piscem-infer .quant file with columns: target_name, ecount, eeln, tpm. " + "This differs from the assumed columns in the original tximport package. " + "If you encounter issues, please provide the column names explicitly." + ) + ) + + id_column = "target_name" if id_column is None else id_column + counts_column = "ecount" if counts_column is None else counts_column + length_column = "eeln" if length_column is None else length_column + abundance_column = "tpm" if abundance_column is None else abundance_column importer = read_tsv elif data_type == "stringtie": diff --git a/pytximport/importers/_read_salmon.py b/pytximport/importers/_read_salmon.py index 02b2b2c..b048a2f 100644 --- a/pytximport/importers/_read_salmon.py +++ b/pytximport/importers/_read_salmon.py @@ -121,17 +121,6 @@ def read_salmon( if not file_path.suffix == ".sf" and not file_path.suffix == ".gz": raise ImportError("Only .sf and .gz files are supported.") - # Unzip the file if it is compressed - if file_path.suffix == ".gz": - try: - with gzip.open(file_path, "rt") as f: - file_content = f.read() - file_path = file_path.with_suffix(".sf") - with open(file_path, "w") as f: - f.write(file_content) - except Exception as e: - raise ImportError(f"Could not unzip the file: {file_path}") from e - transcript_data = read_tsv( file_path, id_column=id_column, diff --git a/test/conftest.py b/test/conftest.py index 69412c2..121f057 100644 --- a/test/conftest.py +++ b/test/conftest.py @@ -89,6 +89,12 @@ def salmon_file() -> Path: return Path(FILE_DIR) / "salmon" / "quant.sf" +@pytest.fixture(scope="session") +def salmon_file_gzip() -> Path: + """Provide the path to a salmon quantification file.""" + return Path(FILE_DIR) / "salmon" / "quant.sf.gz" + + @pytest.fixture(scope="session") def salmon_multiple_files() -> List[Path]: """Create multiple salmon quantification files.""" @@ -100,6 +106,12 @@ def salmon_multiple_files() -> List[Path]: return file_paths +@pytest.fixture(scope="session") +def piscem_file() -> Path: + """Provide the path to a piscem quantification file.""" + return Path(FILE_DIR) / "piscem" / "res.quant" + + @pytest.fixture(scope="session") def fabry_disease_files() -> List[Path]: """Output the paths to the fabry disease files.""" @@ -120,15 +132,20 @@ def fabry_disease_files() -> List[Path]: @pytest.fixture(scope="session") def transcript_name_mapping_human() -> pd.DataFrame: """Provide a transcript id to transcript name mapping for human samples.""" - from pybiomart import Dataset - - dataset = Dataset(name="hsapiens_gene_ensembl", host="http://www.ensembl.org") - transcript_name_mapping_human = dataset.query(attributes=["ensembl_transcript_id", "external_transcript_name"]) - transcript_name_mapping_human.columns = ["transcript_id", "transcript_name"] + transcript_name_mapping_human = pd.read_table( + Path(FILE_DIR) / "transcript_name_mapping_human.tsv", + header=0, + ) return transcript_name_mapping_human +@pytest.fixture(scope="session") +def transcript_name_mapping_human_path() -> Path: + """Provides the path to the transcript id to transcript name mapping for human samples.""" + return Path(FILE_DIR) / "transcript_name_mapping_human.tsv" + + @pytest.fixture(scope="session") def gtf_annotation_file() -> Path: """Provide the path to a GTF annotation file.""" diff --git a/test/data/piscem/res.quant b/test/data/piscem/res.quant new file mode 100644 index 0000000..b32c6c8 --- /dev/null +++ b/test/data/piscem/res.quant @@ -0,0 +1,15 @@ +target_name len eeln tpm ecount +ENST00000513300.5 1924 1746.98 11129.2 102.328 +ENST00000282507.7 2355 2177.98 138884 1592.02 +ENST00000504685.5 1476 1298.98 10041.8 68.6528 +ENST00000243108.4 1733 1555.98 41944.9 343.499 +ENST00000303450.4 1516 1338.98 94221.8 664 +ENST00000243082.4 2039 1861.98 5612.36 55 +ENST00000303406.4 1524 1346.98 42908.2 304.189 +ENST00000303460.4 1936 1758.98 5076.85 47 +ENST00000243056.4 2423 2245.98 3553.05 42 +ENST00000312492.2 1805 1627.98 26609.9 228 +ENST00000040584.5 1889 1711.98 476675 4295 +ENST00000430889.2 1666 1488.98 79578.2 623.628 +ENST00000394331.3 2943 2765.98 5885.85 85.6842 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DUSP10-203 +ENST00000494642 DUSP10-204 +ENST00000665303 LINC01705-206 +ENST00000431729 LINC01705-202 +ENST00000715677 LINC01705-208 +ENST00000433576 LINC01705-203 +ENST00000412445 LINC01705-201 +ENST00000668844 LINC01705-207 +ENST00000658927 LINC01705-205 +ENST00000438158 LINC01705-204 +ENST00000363163 RNU6-403P-201 +ENST00000421147 LINC02474-201 +ENST00000441160 LINC02474-202 +ENST00000412098 LYST-AS1-201 +ENST00000438371 LINC02768-201 +ENST00000715678 LINC02768-203 +ENST00000443207 LINC02768-202 diff --git a/test/test_piscem.py b/test/test_piscem.py new file mode 100644 index 0000000..228a3b2 --- /dev/null +++ b/test/test_piscem.py @@ -0,0 +1,38 @@ +"""Test importing salmon quantification files.""" + +from pathlib import Path +from typing import List + +import anndata as ad +import pandas as pd +import xarray as xr + +from pytximport import tximport +from pytximport.utils import biotype_filters + + +def test_piscem( + piscem_file: Path, + transcript_gene_mapping_human: pd.DataFrame, +) -> None: + """Test importing a piscem quantification file. + + Args: + piscem_file (Path): Path to the piscem quantification file. + transcript_gene_mapping_human (pd.DataFrame): Transcript to gene mapping. + """ + result = tximport( + [piscem_file], + "piscem", + transcript_gene_mapping_human, + output_type="anndata", + ignore_transcript_version=True, + ignore_after_bar=True, + counts_from_abundance=None, # type: ignore + ) + + # Check that the result is an AnnData object + assert isinstance(result, ad.AnnData) + + # Check that the counts.data are all positive + assert (result.X >= 0).all() diff --git a/test/test_salmon.py b/test/test_salmon.py index ecc1fda..28d158f 100644 --- a/test/test_salmon.py +++ b/test/test_salmon.py @@ -19,6 +19,7 @@ def test_salmon( Args: salmon_file (Path): Path to the salmon quantification file. + transcript_gene_mapping_human (pd.DataFrame): Transcript to gene mapping. """ for counts_from_abundance in [None, "scaled_tpm", "length_scaled_tpm"]: for output_type in ["xarray", "anndata"]: @@ -44,6 +45,31 @@ def test_salmon( assert (counts >= 0).all() +def test_salmon_gzip( + salmon_file_gzip: Path, + transcript_gene_mapping_human: pd.DataFrame, +) -> None: + """Test importing a gzipped salmon quantification file. + + Args: + salmon_file_gzip (Path): Path to the gzipped salmon quantification file. + transcript_gene_mapping_human (pd.DataFrame): Transcript to gene mapping. + """ + result = tximport( + [salmon_file_gzip], + "salmon", + transcript_gene_mapping_human, + ignore_transcript_version=True, + ignore_after_bar=True, + ) + + # Check that the result is an AnnData object + assert isinstance(result, ad.AnnData) + + # Check that the counts.data are all positive + assert (result.X >= 0).all() + + def test_multiple_salmon( salmon_multiple_files: List[Path], transcript_gene_mapping_mouse: pd.DataFrame, diff --git a/test/test_transcript_gene_map.py b/test/test_transcript_gene_map.py index 518313e..58faf22 100644 --- a/test/test_transcript_gene_map.py +++ b/test/test_transcript_gene_map.py @@ -12,16 +12,17 @@ def test_transcript_to_gene_map() -> None: """Test creating a transcript to gene map.""" - df_transcript_to_gene = create_transcript_gene_map( - species="human", - host="http://www.ensembl.org", - target_field="external_gene_name", - ) + for species in ["human", "mouse"]: + df_transcript_to_gene = create_transcript_gene_map( + species=species, + host="http://www.ensembl.org", + target_field="external_gene_name", + ) - assert isinstance(df_transcript_to_gene, pd.DataFrame), "The output is not a DataFrame." - assert df_transcript_to_gene.shape[1] == 2, "The output has the wrong number of columns." - assert "transcript_id" in df_transcript_to_gene.columns, "The output is missing the `transcript_id` column." - assert "gene_id" in df_transcript_to_gene.columns, "The output is missing the `gene_id` column." + assert isinstance(df_transcript_to_gene, pd.DataFrame), "The output is not a DataFrame." + assert df_transcript_to_gene.shape[1] == 2, "The output has the wrong number of columns." + assert "transcript_id" in df_transcript_to_gene.columns, "The output is missing the `transcript_id` column." + assert "gene_id" in df_transcript_to_gene.columns, "The output is missing the `gene_id` column." def test_transcript_to_gene_map_from_gtf_annotation( @@ -62,3 +63,13 @@ def test_transcript_to_gene_map_from_gtf_annotation( ), df_transcript_to_gene_reference, ) + + # Test using the transcript name as the source field + df_transcript_to_gene = create_transcript_gene_map_from_annotation( + gtf_annotation_file, + source_field="transcript_name", + target_field="gene_id", + ) + + assert isinstance(df_transcript_to_gene, pd.DataFrame), "The output is not a DataFrame." + assert df_transcript_to_gene.shape[1] == 2, "The output has the wrong number of columns." diff --git a/test/test_transcript_level.py b/test/test_transcript_level.py index 1f3db1f..8b347b1 100644 --- a/test/test_transcript_level.py +++ b/test/test_transcript_level.py @@ -13,12 +13,14 @@ def test_salmon_transcript_level( salmon_file: Path, transcript_name_mapping_human: pd.DataFrame, + transcript_name_mapping_human_path: Path, ) -> None: """Test importing a salmon quantification file at the transcript level. Args: salmon_file (Path): Path to the salmon quantification file. transcript_name_mapping_human (pd.DataFrame): The mapping of transcript ids to transcript names. + transcript_name_mapping_human_path (Path): The path to the transcript name mapping. """ result = tximport( [salmon_file], @@ -37,21 +39,27 @@ def test_salmon_transcript_level( assert (counts >= 0).all() # replace the transcript ids with the transcript names - result = replace_transcript_ids_with_names(result, transcript_name_mapping_human) + result_df = replace_transcript_ids_with_names(result, transcript_name_mapping_human) # Check that the result is an AnnData object - assert isinstance(result, ad.AnnData) + assert isinstance(result_df, ad.AnnData) # Check that the var names don't start with ENST - assert result.var_names.str.startswith("ENST").sum() == 0 + assert result_df.var_names.str.startswith("ENST").sum() == 0 # Check that the var names are not nan or the string "nan" or empty assert ( - result.var_names.isna().sum() == 0 - and (result.var_names == "nan").sum() == 0 - and (result.var_names == "").sum() == 0 + result_df.var_names.isna().sum() == 0 + and (result_df.var_names == "nan").sum() == 0 + and (result_df.var_names == "").sum() == 0 ) + # Check that it also works with a path to the transcript name mapping + result_path = replace_transcript_ids_with_names(result, transcript_name_mapping_human_path) + + # Check that the results are the same + pd.testing.assert_frame_equal(result_df.var_names.to_frame(), result_path.var_names.to_frame()) + def test_dtu_scaled_tpm( salmon_file: Path,