diff --git a/MANIFEST.in b/MANIFEST.in
index fc4c9ca0..906f1d82 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,4 +1,5 @@
include README.md
+exclude tests
graft tiny
prune **/__pycache__
prune **/*_Outputs
diff --git a/README.md b/README.md
index 57006663..91b7d4df 100644
--- a/README.md
+++ b/README.md
@@ -90,12 +90,12 @@ tiny get-template
### Requirements for User-Provided Input Files
-| Input Type | File Extension | Requirements |
-|----------------------------------------------------------------------------|-------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| Reference annotations
[(example)](START_HERE/reference_data/ram1.gff3) | GFF3 / GFF2 / GTF | Column 9 attributes (defined as "tag=value" or "tag "):- Each feature's `ID` tag is required
- Feature classes can be defined with the `Class` tag. If undefined, the default value \__UNKNOWN_\_ will be used.
- Discontinuous features must be defined with the `Parent` tag whose value is the logical parent's `ID`, or by sharing the same `ID`.
- Attribute values containing commas must represent lists
- All features must be stranded
- See the example link (left) for col. 9 formatting
|
-| Sequencing data
[(example)](START_HERE/fastq_files) | FASTQ(.gz) | Files must be demultiplexed. |
-| Reference genome
[(example)](START_HERE/reference_data/ram1.fa) | FASTA | Chromosome identifiers (e.g. Chr1): - Must match your reference annotation file chromosome identifiers
- Are case sensitive
|
-| Bowtie indexes (optional) 1 | ebwt | Must be small indexes (.ebwtl indexes are not supported) |
+| Input Type | File Extension | Requirements |
+|----------------------------------------------------------------------------|-------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| Reference annotations
[(example)](START_HERE/reference_data/ram1.gff3) | GFF3 / GFF2 / GTF | Column 9 attributes (defined as "tag=value" or "tag "):- Each feature must have an `ID` or `gene_id` tag.
- Feature classes can be defined with the `Class` tag. If undefined, the default value \__UNKNOWN_\_ will be used.
- Discontinuous features must be defined with the `Parent` tag whose value is the logical parent's `ID`, or by sharing the same `ID`.
- Attribute values containing commas must represent lists.
- All features must be stranded.
- See the example link (left) for col. 9 formatting.
|
+| Sequencing data
[(example)](START_HERE/fastq_files) | FASTQ(.gz) | Files must be demultiplexed. |
+| Reference genome
[(example)](START_HERE/reference_data/ram1.fa) | FASTA | Chromosome identifiers (e.g. Chr1): - Must match your reference annotation file chromosome identifiers
- Are case sensitive
|
+| Bowtie indexes (optional) 1 | ebwt | Must be small indexes (.ebwtl indexes are not supported) |
1 Bowtie indexes can be created for you. See the [configuration file documentation](doc/Configuration.md#building-bowtie-indexes).
diff --git a/START_HERE/run_config.yml b/START_HERE/run_config.yml
index ea9d4aa3..9de0e9cc 100644
--- a/START_HERE/run_config.yml
+++ b/START_HERE/run_config.yml
@@ -244,6 +244,13 @@ counter_source_filter: []
##-- If source AND type filters are given, a line must match both to be included --##
counter_type_filter: []
+##-- Select the StepVector implementation that is used. Options: HTSeq or Cython --##
+counter_stepvector: 'Cython'
+
+##-- If False: a feature with multiple values in its ID attribute is treated as an error --##
+##-- If True: multiple ID values are allowed, but only the first value is used --##
+counter_allow_multi_id: True
+
##-- If True: produce diagnostic logs to indicate what was eliminated and why --##
counter_diags: False
diff --git a/conda/conda-linux-64.lock b/conda/conda-linux-64.lock
index df6acb44..88ba3f65 100644
--- a/conda/conda-linux-64.lock
+++ b/conda/conda-linux-64.lock
@@ -1,23 +1,22 @@
# Generated by conda-lock.
# platform: linux-64
-# input_hash: d9433cf548826db3a4d918dce3ebcfa5793ad683ff22014c94c1796381c86f17
+# input_hash: ef26dba2670179c6605442a613aa0567cc43b352efe64eaefbb5399ddc41e110
@EXPLICIT
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
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-https://conda.anaconda.org/main/linux-64/ca-certificates-2022.07.19-h06a4308_0.tar.bz2#ef4b29ea120fdfa542adbce43d035c95
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.9.24-ha878542_0.tar.bz2#41e4e87062433e283696cf384f952ef6
https://conda.anaconda.org/main/noarch/font-ttf-dejavu-sans-mono-2.37-hd3eb1b0_0.tar.bz2#801b4743a301a4e11cbd9609d418e101
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-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-3.0.0-1.tar.bz2#d7c7e92a8ccc518709474dd3eda896b9
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-devel_linux-64-9.5.0-h367e8d2_16.tar.bz2#b2f784aca08d3e45288c8ea6c7602b86
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+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-devel_linux-64-9.5.0-h367e8d2_16.tar.bz2#e5cfd476f10829efccf955635377cfba
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https://conda.anaconda.org/conda-forge/linux-64/mscorefonts-0.0.1-2.tar.bz2#c9fd57fc9f2c51ff7b049b64fba8a7df
-https://conda.anaconda.org/main/noarch/tzdata-2022a-hda174b7_0.tar.bz2#a99750e9650510d276b56d2b000f4569
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2022d-h191b570_0.tar.bz2#456b5b1d99e7a9654b331bcd82e71042
https://conda.anaconda.org/main/noarch/fonts-anaconda-1-h8fa9717_0.tar.bz2#7a445a2d9fbe2a88de8f09e9527f4ce1
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@@ -28,10 +27,9 @@ https://conda.anaconda.org/main/noarch/fonts-conda-ecosystem-1-hd3eb1b0_0.tar.bz
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-https://conda.anaconda.org/main/linux-64/brotli-1.0.9-he6710b0_2.tar.bz2#bdc971e2a9affb5125b68ad708172dab
https://conda.anaconda.org/main/linux-64/bzip2-1.0.8-h7b6447c_0.tar.bz2#f52e60deb7f4c82821be9a868e889348
https://conda.anaconda.org/main/linux-64/c-ares-1.18.1-h7f8727e_0.tar.bz2#62ca289a9704ed465d3324295ef851d9
-https://conda.anaconda.org/conda-forge/linux-64/expat-2.4.8-h27087fc_0.tar.bz2#e1b07832504eeba765d648389cc387a9
+https://conda.anaconda.org/main/linux-64/expat-2.4.9-h6a678d5_0.tar.bz2#d254ca6cf5c657cecd6912b0671379cd
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@@ -40,52 +38,53 @@ https://conda.anaconda.org/conda-forge/linux-64/icu-68.2-h9c3ff4c_0.tar.bz2#6618
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+https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f
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diff --git a/conda/conda-osx-64.lock b/conda/conda-osx-64.lock
index 0fb89978..f0653de9 100644
--- a/conda/conda-osx-64.lock
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https://conda.anaconda.org/bioconda/noarch/bioconductor-summarizedexperiment-1.24.0-r41hdfd78af_0.tar.bz2#f21eb229b8ee58680cb0179ef6d51f7e
-https://conda.anaconda.org/conda-forge/noarch/cwltool-3.1.20220628170238-pyhc268e32_0.tar.bz2#b8780347d56585db8c9323522cbe9118
https://conda.anaconda.org/conda-forge/noarch/r-rematch2-2.1.2-r41hc72bb7e_1.tar.bz2#5c26fbf849007fc5022745ec14e38822
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@@ -290,4 +289,4 @@ https://conda.anaconda.org/bioconda/osx-64/bioconductor-genefilter-1.76.0-r41h11
https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.72.0-r41hdfd78af_0.tar.bz2#32c0e22a0095ad9b592a6bf7e16a835a
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-https://conda.anaconda.org/bioconda/osx-64/bioconductor-deseq2-1.34.0-r41h7cba510_1.tar.bz2#75a3a591545cbbd603be67ec35c43af8
+https://conda.anaconda.org/bioconda/osx-64/bioconductor-deseq2-1.34.0-r41hb890f52_2.tar.bz2#480ff3b340d91e3a4fff6c65a0d22715
diff --git a/conda/environment.yml b/conda/environment.yml
index 3afc17d8..99f0d099 100644
--- a/conda/environment.yml
+++ b/conda/environment.yml
@@ -6,6 +6,7 @@ dependencies:
- python>=3.9
- bioconductor-deseq2==1.34.0
- bowtie==1.3.1
+ - cython==0.29.24
- fastp==0.23.2
- htseq==2.0.2
- nodejs==16.13.1
diff --git a/doc/Parameters.md b/doc/Parameters.md
index aec57919..b8ca2d63 100644
--- a/doc/Parameters.md
+++ b/doc/Parameters.md
@@ -63,14 +63,14 @@ Optional arguments:
## tiny-count
-### All-Features
+### All Features
| Run Config Key | Commandline Argument |
|------------------------|------------------------|
| counter_all_features: | `--all-features` |
By default, tiny-count will only evaluate alignments to features which match a `Select for...` & `with value...` of at least one rule in your Features Sheet. It is this matching feature set, and only this set, which is included in `feature_counts.csv` and therefore available for analysis by tiny-deseq.r and tiny-plot. Switching this option "on" will include all features in every input GFF file, regardless of attribute matches, for tiny-count and downstream steps.
-### Normalize-by-Hits
+### Normalize by Hits
| Run Config Key | Commandline Argument |
|----------------------------|---------------------------|
| counter-normalize-by-hits: | `--normalize-by-hits T/F` |
@@ -92,6 +92,20 @@ The SAM files produced by the tinyRNA pipeline are collapsed by default; alignme
You can optionally filter features in your GFF files by specifying sources and/or types that are desired. Source and type refer to GFF columns 2 and 3 respectively. If source _and_ type filters are specified, each feature must match one of the sources _and_ one of the types in order to be included in the counting process. For both filters, an empty list is the same as "allow all."
+### StepVector
+| Run Config Key | Commandline Argument |
+|--------------------|----------------------|
+| counter_stepvector | `--stepvector` |
+
+A custom Cython implementation of HTSeq's StepVector is used for finding features that overlap each alignment interval. While the core C++ component of the StepVector is the same, we have found that our Cython implementation can result in runtimes up to 50% faster than HTSeq's implementation. This parameter allows you to use HTSeq's StepVector if you wish (for example, if the Cython StepVector is incompatible with your system)
+
+### Allow Features with Multiple ID Values
+ | Run Config Key | Commandline Argument |
+|------------------------|----------------------|
+| counter_allow_multi_id | `--multi-id` |
+
+By default, an error will be produced if a GFF file contains a feature with multiple comma separated values listed under its ID attribute. Switching this option "on" instructs tiny-count to accept these features without error, but only the first listed value is used as the ID.
+
### Is Pipeline
| Run Config Key | Commandline Argument |
|----------------|----------------------|
@@ -127,10 +141,10 @@ Required arguments:
Optional arguments:
-h, --help show this help message and exit
- -sf [SOURCE [SOURCE ...]], --source-filter [SOURCE [SOURCE ...]]
+ -sf [SOURCE ...], --source-filter [SOURCE ...]
Only produce counts for features whose GFF column 2
matches the source(s) listed
- -tf [TYPE [TYPE ...]], --type-filter [TYPE [TYPE ...]]
+ -tf [TYPE ...], --type-filter [TYPE ...]
Only produce counts for features whose GFF column 3
matches the type(s) listed
-nh T/F, --normalize-by-hits T/F
@@ -139,6 +153,12 @@ Optional arguments:
-dc, --decollapse Create a decollapsed copy of all SAM files listed in
your Samples Sheet. This option is ignored for non-
collapsed inputs.
+ -sv {Cython,HTSeq}, --stepvector {Cython,HTSeq}
+ Select which StepVector implementation is used to find
+ features overlapping an interval.
+ -md, --multi-id Don't treat features with multiple ID values as an
+ error. Only the first value will be used as the
+ feature's ID.
-a, --all-features Represent all features in output counts table, even if
they did not match a Select for / with value.
-p, --is-pipeline Indicates that tiny-count was invoked as part of a
diff --git a/doc/tiny-count.md b/doc/tiny-count.md
index de66cce8..1439c635 100644
--- a/doc/tiny-count.md
+++ b/doc/tiny-count.md
@@ -118,6 +118,7 @@ You may encounter the following cases when you have more than one unique GFF fil
- If a feature is defined in one GFF file, then again but under a different **Alias by...**, then both aliases are retained and treated as a list. All aliases will be present in the `Feature Name` column of the Feature Counts output table. They will be comma separated.
Discontinuous features and feature filtering support:
-- Discontinuous features are supported (as defined by the `Parent` attribute key, or by a shared `ID` attribute value). Rule and alias matches of descendents are merged with the root parent's.
+- Discontinuous features are supported (as defined by the `Parent` attribute key, or by a shared `ID`/`gene_id` attribute value). Rule and alias matches of descendents are merged with the root parent's.
+- If a feature contains both `ID` and `gene_id` attributes, only the value of `ID` is used as the feature's ID.
- Features can be filtered during GFF parsing by their `source` and/or `type` columns, and these preferences can be specified in the Run Config file. These are inclusive filters. Only features matching the values specified will be retained for selection and listed in the output counts table. An empty list allows all values. See the [parameters documentation](Parameters.md#filters) for information about specifying these filters.
- If a filtered feature breaks a feature lineage (that is, features chained via the `Parent` attribute), then the highest non-filtered ancestor is designated the root parent. The lineage is maintained transparently but the filtered feature does not contribute to the domains of selection.
\ No newline at end of file
diff --git a/doc/tiny-plot.md b/doc/tiny-plot.md
index a8e890d8..8b60d37a 100644
--- a/doc/tiny-plot.md
+++ b/doc/tiny-plot.md
@@ -70,8 +70,8 @@ Features can have multiple classes associated with them, so it is useful to see
-#### Class N
-Class **N** represents the percentage of mapped reads that were unassigned. Sources of unassigned reads include:
+#### Class \_UNASSIGNED_
+This category represents the percentage of mapped reads that were unassigned. Sources of unassigned reads include:
- A lack of features passing selection at alignment loci
- Alignments which do not overlap with any features
diff --git a/setup.py b/setup.py
index df524016..0f83abb4 100644
--- a/setup.py
+++ b/setup.py
@@ -4,6 +4,7 @@
import setuptools
from setuptools.command.install import install
+from Cython.Build import cythonize
# Package metadata
NAME = 'tinyrna'
@@ -14,20 +15,80 @@
PLATFORM = 'Unix'
REQUIRES_PYTHON = '>=3.9.0'
VERSION = '1.0'
+REQUIRED = [] # Required packages are installed via Conda's environment.yml
-# Required packages are installed via Conda's environment.yml
-# See PreFlight below...
-REQUIRED = []
+class PrereqAndExec(install):
+ """These checks are performed prior to installation to ensure that this setup routine
+ is only executed within a Conda environment. Users should perform installation via
+ setup.sh, not setup.py."""
-class PreFlight(install):
def run(self):
- if not all([os.getenv(conda_var) for conda_var in ["CONDA_PREFIX", "CONDA_DEFAULT_ENV"]]):
- sys.exit("CRITICAL ERROR: you appear to be installing %s outside of a conda environment.\n"
- "Instead, please run: ./setup.sh" % (NAME,))
+ if not self.in_conda_env():
+ sys.exit("CRITICAL ERROR: you appear to be installing %s outside of a conda environment.\n" % (NAME,) +
+ "Instead, please run: ./setup.sh" )
else:
install.run(self)
+ def in_conda_env(self):
+ return all([os.getenv(conda_var) for conda_var in ["CONDA_PREFIX", "CONDA_DEFAULT_ENV"]])
+
+
+def get_cython_extension_defs():
+ """Returns a list of Extension objects corresponding to the contents of pyx_files.
+ Extensions indicated as optional in pyx_files will NOT cause the installation to
+ error out if there are build issues, and therefore must be used as optional imports."""
+
+ pyx_files = [
+ # (file path, optional)
+ ('tiny/rna/counter/stepvector/_stepvector.pyx', True),
+ ('tests/cython_tests/stepvector/test_cython.pyx', True)
+ ]
+
+ cxx_extension_args = {
+ 'extra_compile_args': ['-std=c++11', '-O3'],
+ 'extra_link_args': [],
+ 'language': 'c++'
+ }
+
+ if sys.platform == "darwin" and os.getenv('SDKROOT') is None:
+ # If building with the environment variables set by Conda, this isn't necessary
+ # However build shortcuts in some IDEs will strip these vars
+ sdk_root = get_macos_sdk_path()
+ cxx_extension_args['extra_compile_args'] += ['-isystem', os.path.join(sdk_root, '/usr/include')]
+ cxx_extension_args['extra_link_args'] += ['-L' + os.path.join(sdk_root, '/usr/lib')]
+
+ return [setuptools.Extension(
+ pyx_filename.replace('./', '').replace('/', '.').rstrip('.pyx'),
+ sources=[pyx_filename],
+ optional=optional,
+ **cxx_extension_args)
+ for pyx_filename, optional in pyx_files]
+
+
+def get_macos_sdk_path():
+ """Determines the SDK path for compiler dependencies in a manner that will be
+ compatible with conda-build pipelines. The following code was copied from
+ https://github.com/python-pillow/Pillow/blob/main/setup.py """
+
+ try:
+ import subprocess
+ sdk_path = subprocess.check_output(["xcrun", "--show-sdk-path"]).strip().decode('latin1')
+ except Exception:
+ sdk_path = None
+
+ xcode_sdk_path = "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk"
+ commandlinetools_sdk_path = "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk"
+
+ if not sdk_path or sdk_path == xcode_sdk_path:
+ if os.path.exists(commandlinetools_sdk_path):
+ sdk_path = commandlinetools_sdk_path
+ else:
+ raise RuntimeError("The macOS SDK path could not be found. This is required for Cython. "
+ "Please run xcode-select --install in your terminal.")
+
+ return sdk_path
+
setuptools.setup(
name=NAME,
@@ -35,7 +96,7 @@ def run(self):
author=AUTHOR,
author_email=EMAIL,
description=DESCRIPTION,
- cmdclass={'install': PreFlight},
+ cmdclass={'install': PrereqAndExec},
include_package_data=True,
packages=['tiny'],
zip_safe=False,
@@ -48,6 +109,11 @@ def run(self):
'tiny-plot = tiny.rna.plotter:main'
]
},
+ ext_modules=cythonize(
+ get_cython_extension_defs(),
+ compiler_directives={'language_level': '3'},
+ gdb_debug=False
+ ),
scripts=['tiny/rna/tiny-deseq.r'],
classifiers=[
'Programming Language :: Python :: 3',
diff --git a/setup.sh b/setup.sh
index 56ead387..8834649c 100755
--- a/setup.sh
+++ b/setup.sh
@@ -58,7 +58,7 @@ function setup_environment() {
# Setup tinyRNA environment using our generated lock file
status "Setting up $env_name environment (this may take a while)..."
conda create --file $platform_lock_file --name $env_name 2>&1 | tee "env_install.log"
- if ! grep -q "Executing transaction: ...working... done" env_install.log; then
+ if ! tr -d \\n < env_install.log | grep -q "Executing transaction: ...working... done"; then
fail "$env_name environment setup failed"
echo "Console output has been saved to env_install.log."
exit 1
@@ -67,6 +67,21 @@ function setup_environment() {
fi
}
+function setup_macOS_command_line_tools() {
+ # Install Xcode command line tools if necessary
+ if ! xcode-select --print-path > /dev/null 2>&1; then
+ status "Installing Xcode command line tools. Follow prompts in new window..."
+ if xcode-select --install; then
+ success "Command line tools setup complete"
+ else
+ fail "Command line tools installation failed"
+ exit 1
+ fi
+ else
+ success "Xcode command line tools are already installed"
+ fi
+}
+
################################################################################
# Main Routine
################################################################################
@@ -82,6 +97,7 @@ if [[ "$OSTYPE" == "darwin"* ]]; then
shell=$(basename "$(dscl . -read ~/ UserShell | cut -f 2 -d " ")")
miniconda_installer="Miniconda3-py${python_version/./}_${miniconda_version}-MacOSX-x86_64.sh"
platform_lock_file="./conda/conda-osx-64.lock"
+ setup_macOS_command_line_tools
elif [[ "$OSTYPE" == "linux-gnu" ]]; then
success "Linux detected"
shell="$(basename "$SHELL")"
@@ -135,7 +151,7 @@ if conda env list | grep -q "$env_name"; then
echo
status "Updating $env_name environment..."
conda update --file $platform_lock_file --name "$env_name" 2>&1 | tee "env_update.log"
- if ! grep -q "Executing transaction: ...working... done" env_update.log; then
+ if ! tr -d \\n < env_install.log | grep -q "Executing transaction: ...working... done"; then
fail "Failed to update the environment"
echo "Check the env_update.log file for more information."
exit 1
diff --git a/tests/cython_tests/__init__.py b/tests/cython_tests/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/cython_tests/stepvector/Makefile b/tests/cython_tests/stepvector/Makefile
new file mode 100755
index 00000000..35b0756d
--- /dev/null
+++ b/tests/cython_tests/stepvector/Makefile
@@ -0,0 +1,15 @@
+CXX := clang++
+
+PY_VERS := python3.9
+PY_CFLAGS := $(shell ${PY_VERS}-config --cflags --libs)
+PY_LDFLAGS := $(shell ${PY_VERS}-config --ldflags --embed)
+
+INCLUDE := -I$(realpath ../../../tiny/rna/counter/stepvector/src)
+LDFLAGS := ${PY_LDFLAGS} -L${CONDA_PREFIX}/lib -rpath ${CONDA_PREFIX}/lib
+CXXFLAGS := -std=c++17 -stdlib=libc++ ${INCLUDE} ${PY_CFLAGS}
+
+test_core : test_core.cpp
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) $^ -o $@
+
+clean :
+ @rm -f test_core
\ No newline at end of file
diff --git a/tests/cython_tests/stepvector/__init__.py b/tests/cython_tests/stepvector/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/cython_tests/stepvector/test_core.cpp b/tests/cython_tests/stepvector/test_core.cpp
new file mode 100644
index 00000000..895f8f35
--- /dev/null
+++ b/tests/cython_tests/stepvector/test_core.cpp
@@ -0,0 +1,51 @@
+#include "StepVector.h"
+#include "PyRef.h"
+
+using sparse_vectors::_StepVector;
+using PyPtr::PyRef;
+
+int main(){
+ Py_Initialize();
+
+ _StepVector sv;
+
+ PyObject *c1 = PySet_New(NULL); // {featA, featB}
+ PyObject *c2 = PySet_New(NULL); // {featC}
+ PyObject *c3 = PySet_New(NULL); // {featD}
+
+ PyObject *sA = PyUnicode_FromString("featA");
+ PyObject *sB = PyUnicode_FromString("featB");
+ PyObject *sC = PyUnicode_FromString("featC");
+ PyObject *sD = PyUnicode_FromString("featD");
+
+ PySet_Add(c1, sA);
+ PySet_Add(c1, sB);
+ PySet_Add(c2, sC);
+ PySet_Add(c3, sD);
+
+ PyRef p1 = PyRef(c1);
+ PyRef p2 = PyRef(c2);
+ PyRef p3 = PyRef(c3);
+
+ sv.add_value(0, 10, p1);
+ sv.add_value(8, 15, p2);
+ sv.add_value(9, 20, p3);
+
+ std::cout << std::endl;
+
+ for (auto it = sv.get_values(-1); it != sv.end(); ++it){
+ std::cout << it->first << ": ";
+ PyObject_Print(it->second.get(), stdout, 0);
+ std::cout << std::endl;
+ }
+
+ /* Expect:
+ -9223372036854775808: set()
+ 0: {'featA', 'featB'}
+ 8: {'featA', 'featC', 'featB'}
+ 9: {'featD', 'featA', 'featC', 'featB'}
+ 11: {'featD', 'featC'}
+ 16: {'featD'}
+ 21: set()
+ */
+}
\ No newline at end of file
diff --git a/tests/cython_tests/stepvector/test_cython.pyx b/tests/cython_tests/stepvector/test_cython.pyx
new file mode 100644
index 00000000..7a7e15c9
--- /dev/null
+++ b/tests/cython_tests/stepvector/test_cython.pyx
@@ -0,0 +1,54 @@
+# distutils: language = c++
+# cython: language_level = 3
+import sys
+
+from cpython.ref cimport PyObject
+from libcpp.pair cimport pair
+from cython.operator cimport dereference as deref, preincrement as inc, postincrement as pinc
+
+from tiny.rna.counter.stepvector._stepvector cimport _StepVector, PyRef
+ctypedef PyObject* PyPtr
+
+def main():
+ cdef PyRef p1, p2, p3
+
+ sv = new _StepVector[PyRef]()
+
+ c1 = {"featA", "featB"}
+ c2 = {"featC"}
+ c3 = {"featD"}
+ p1 = PyRef(c1)
+ p2 = PyRef(c2)
+ p3 = PyRef(c3)
+
+ sv.add_value(0, 10, p1)
+ sv.add_value(8, 15, p2)
+ sv.add_value(9, 20, p3)
+
+ it = sv.get_values(-1)
+ expected = iter([
+ ((-1 * sys.maxsize - 1), set()),
+ (0, {'featA', 'featB'}),
+ (8, {'featA', 'featB', 'featC'}),
+ (9, {'featA', 'featB', 'featC', 'featD'}),
+ (11, {'featC', 'featD'}),
+ (16, {'featD'}),
+ (21, set())
+ ])
+
+ while it != sv.end():
+ step = deref(pinc(it))
+ exp_pos, exp_set = next(expected)
+
+ try:
+ assert step.first == exp_pos
+ assert