cool-seq-tool 0.8.0__tar.gz → 0.9.0__tar.gz

{cool_seq_tool-0.8.0 → cool_seq_tool-0.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cool_seq_tool
-Version: 0.8.0
+Version: 0.9.0
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -53,7 +53,7 @@ Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic==2.*
 Requires-Dist: ga4gh.vrs~=2.0.0a10
-Requires-Dist: wags-tails~=0.1.3
+Requires-Dist: wags-tails~=0.2.2
 Requires-Dist: bioutils
 Provides-Extra: dev
 Requires-Dist: pre-commit>=3.7.1; extra == "dev"
@@ -61,11 +61,11 @@ Requires-Dist: ipython; extra == "dev"
 Requires-Dist: ipykernel; extra == "dev"
 Requires-Dist: psycopg2-binary; extra == "dev"
 Requires-Dist: ruff==0.5.0; extra == "dev"
-Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: pytest-cov; extra == "test"
-Requires-Dist: pytest-asyncio==0.18.3; extra == "test"
-Requires-Dist: mock; extra == "test"
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Requires-Dist: pytest-asyncio==0.18.3; extra == "tests"
+Requires-Dist: mock; extra == "tests"
 Provides-Extra: docs
 Requires-Dist: sphinx==6.1.3; extra == "docs"
 Requires-Dist: sphinx-autodoc-typehints==1.22.0; extra == "docs"
@@ -76,10 +76,10 @@ Requires-Dist: furo==2023.3.27; extra == "docs"
 Requires-Dist: sphinx-github-changelog==1.2.1; extra == "docs"
 
 <h1 align="center">
-CoolSeqTool
+Cool-Seq-Tool
 </h1>
 
-[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
+[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14007783.svg)](https://doi.org/10.5281/zenodo.14007783) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
 
 ---
 
@@ -90,18 +90,18 @@ CoolSeqTool
 ## Overview
 
 <!-- description -->
-The **CoolSeqTool** provides:
+The Common Operations On Lots-Of Sequences Tool, **Cool-Seq-Tool**, provides:
 
- - A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, [MANE transcript](https://www.ncbi.nlm.nih.gov/refseq/MANE/) descriptions, and the [Universal Transcript Archive](https://github.com/biocommons/uta)
- - Augmented access to the [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, including multiple additional methods and tools
- - Mapping tools that combine the above to support translation between references sequences, annotation layers, and MANE transcripts
+- A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, [MANE transcript](https://www.ncbi.nlm.nih.gov/refseq/MANE/) descriptions, and transcript alignment data from the [Universal Transcript Archive](https://github.com/biocommons/uta)
+- Augmented access to the [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, including multiple additional methods and tools
+- Mapping tools, including a transcript selection algorithm for selecting a representative transcript defined [here](https://coolseqtool.readthedocs.io/stable/transcript_selection.html), that combine the above to support translation between references sequences, annotation layers, and transcripts
 <!-- /description -->
 
 ---
 
 ## Install
 
-CoolSeqTool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
+Cool-Seq-Tool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
 
 ```shell
 python3 -m pip install cool-seq-tool
@@ -113,7 +113,7 @@ See the [installation instructions](https://coolseqtool.readthedocs.io/stable/in
 
 ## Usage
 
-All CoolSeqTool resources can be initialized by way of a top-level class instance:
+All Cool-Seq-Tool resources can be initialized by way of a top-level class instance:
 
 ```pycon
 >>> from cool_seq_tool import CoolSeqTool

cool_seq_tool-0.9.0/README.md

@@ -0,0 +1,59 @@
+<h1 align="center">
+Cool-Seq-Tool
+</h1>
+
+[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14007783.svg)](https://doi.org/10.5281/zenodo.14007783) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
+
+---
+
+**[Documentation](https://coolseqtool.readthedocs.io/stable/)** · [Installation](https://coolseqtool.readthedocs.io/stable/install.html) · [Usage](https://coolseqtool.readthedocs.io/stable/usage.html) · [API reference](https://coolseqtool.readthedocs.io/stable/reference/index.html)
+
+---
+
+## Overview
+
+<!-- description -->
+The Common Operations On Lots-Of Sequences Tool, **Cool-Seq-Tool**, provides:
+
+- A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, [MANE transcript](https://www.ncbi.nlm.nih.gov/refseq/MANE/) descriptions, and transcript alignment data from the [Universal Transcript Archive](https://github.com/biocommons/uta)
+- Augmented access to the [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, including multiple additional methods and tools
+- Mapping tools, including a transcript selection algorithm for selecting a representative transcript defined [here](https://coolseqtool.readthedocs.io/stable/transcript_selection.html), that combine the above to support translation between references sequences, annotation layers, and transcripts
+<!-- /description -->
+
+---
+
+## Install
+
+Cool-Seq-Tool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
+
+```shell
+python3 -m pip install cool-seq-tool
+```
+
+See the [installation instructions](https://coolseqtool.readthedocs.io/stable/install.html) in the documentation for a description of dependency setup requirements.
+
+---
+
+## Usage
+
+All Cool-Seq-Tool resources can be initialized by way of a top-level class instance:
+
+```pycon
+>>> from cool_seq_tool import CoolSeqTool
+>>> from cool_seq_tool.schemas import AnnotationLayer, CoordinateType
+>>> cst = CoolSeqTool()
+>>> result = await cst.mane_transcript.get_mane_transcript(
+...     "NP_004324.2",
+...     599,
+...     AnnotationLayer.PROTEIN,
+...     coordinate_type=CoordinateType.INTER_RESIDUE,
+... )
+>>> result.gene, result.refseq, result.status
+('EGFR', 'NM_005228.5', <TranscriptPriority.MANE_SELECT: 'mane_select'>)
+```
+
+---
+
+## Feedback and contributing
+
+We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The [documentation](https://coolseqtool.readthedocs.io/stable/contributing.html) contains guidance for submitting feedback and contributing new code.

{cool_seq_tool-0.8.0 → cool_seq_tool-0.9.0}/docs/source/contributing.rst

@@ -17,7 +17,7 @@ Create a virtual environment and install :ref:`all dependency groups<dependency-
 
     python3 -m venv venv
     source venv/bin/activate
-    python3 -m pip install -e ".[dev,test,docs]"
+    python3 -m pip install -e ".[dev,tests,docs]"
 
 We use `pre-commit <https://pre-commit.com/#usage>`_ to run conformance tests before commits. This provides checks for:
 

{cool_seq_tool-0.8.0 → cool_seq_tool-0.9.0}/docs/source/index.rst

@@ -16,15 +16,15 @@ Cool-Seq-Tool |version|
    :alt: tests status
    :target: https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml
 
-The **CoolSeqTool** provides:
+The Common Operations On Lots-Of Sequences Tool, **Cool-Seq-Tool**, provides:
 
-* A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, `MANE transcript <https://www.ncbi.nlm.nih.gov/refseq/MANE/>`_ descriptions, and the `Universal Transcript Archive <https://github.com/biocommons/uta>`_
+* A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, `MANE transcript <https://www.ncbi.nlm.nih.gov/refseq/MANE/>`_ descriptions, and transcript alignment data from the `Universal Transcript Archive <https://github.com/biocommons/uta>`_
 * Augmented access to the `SeqRepo <https://github.com/biocommons/biocommons.seqrepo>`_ database, including multiple additional methods and tools
-* Mapping tools that combine the above to support translation between various references sequences and annotation layers, and to MANE-designated transcripts
+* Mapping tools, including a transcript selection algorithm for selecting a representative transcript defined :ref:`here <transcript_selection_policy>`, that combine the above to support translation between various references sequences and annotation layers, and transcripts
 
 See the :ref:`Installation <installation>` and :ref:`Usage <usage>` pages for information on getting started. Individual classes and methods are documented within the :ref:`API reference <api_reference>`.
 
-CoolSeqTool was created to support the `Knowledgebase Integration Project <https://cancervariants.org/projects/integration/>`_ of the `Variant Interpretation for Cancer Consortium (VICC) <https://cancervariants.org/>`_. It is developed primarily by the `Wagner Lab <https://www.nationwidechildrens.org/specialties/institute-for-genomic-medicine/research-labs/wagner-lab>`_. Full source code is available on `GitHub <https://github.com/genomicmedlab/cool-seq-tool>`_.
+Cool-Seq-Tool was created to support the `Knowledgebase Integration Project <https://cancervariants.org/projects/integration/>`_ of the `Variant Interpretation for Cancer Consortium (VICC) <https://cancervariants.org/>`_. It is developed primarily by the `Wagner Lab <https://www.nationwidechildrens.org/specialties/institute-for-genomic-medicine/research-labs/wagner-lab>`_. Full source code is available on `GitHub <https://github.com/genomicmedlab/cool-seq-tool>`_.
 
 .. toctree::
    :hidden:

{cool_seq_tool-0.8.0 → cool_seq_tool-0.9.0}/docs/source/install.rst

@@ -24,7 +24,7 @@ Install Cool-Seq-Tool from `PyPI <https://pypi.org/project/cool-seq-tool/>`_:
    Cool-Seq-Tool provides extra dependency groups for development and testing purposes. Most users won't need to install them.
 
    * ``dev`` includes packages for linting and performing other kinds of quality checks
-   * ``test`` includes packages for running tests
+   * ``tests`` includes packages for running tests
    * ``docs`` includes packages for writing and building documentation
 
 Set up UTA

{cool_seq_tool-0.8.0 → cool_seq_tool-0.9.0}/docs/source/transcript_selection.rst

@@ -28,8 +28,9 @@ All compatible transcripts are evaluated and ordered against the below criteria.
 #. Transcript is annotated as a `MANE Select` transcript
 #. Transcript is annotated as a `MANE Plus Clinical` transcript
 #. Transcript is the longest-compatible remaining transcript
-#. Transcript is the first-published (lowest-numbered RefSeq/Ensembl accession) remaining transcript
 
-.. note::
+   #. If there is a tie, choose the first-published (lowest-numbered RefSeq/Ensembl accession) transcript
 
-   We always prefer the most recent version of a transcript associated with an assembly.
+   .. note::
+
+      We always prefer the most recent version of a transcript associated with an assembly.

{cool_seq_tool-0.8.0 → cool_seq_tool-0.9.0}/docs/source/usage.rst

@@ -30,7 +30,7 @@ Descriptions and examples of functions can be found in the :ref:`API Reference <
 
 .. note::
 
-   Many component classes in CoolSeqTool, including :py:class:`UtaDatabase <cool_seq_tool.sources.uta_database.UtaDatabase>`, :py:class:`ExonGenomicCoordsMapper <cool_seq_tool.mappers.exon_genomic_coords.ExonGenomicCoordsMapper>`, and :py:class:`ManeTranscript <cool_seq_tool.mappers.mane_transcript>`, define public methods as ``async``. This means that, when used inside another function, they must be called with ``await``:
+   Many component classes in Cool-Seq-Tool, including :py:class:`UtaDatabase <cool_seq_tool.sources.uta_database.UtaDatabase>`, :py:class:`ExonGenomicCoordsMapper <cool_seq_tool.mappers.exon_genomic_coords.ExonGenomicCoordsMapper>`, and :py:class:`ManeTranscript <cool_seq_tool.mappers.mane_transcript>`, define public methods as ``async``. This means that, when used inside another function, they must be called with ``await``:
 
    .. code-block:: python
 

{cool_seq_tool-0.8.0 → cool_seq_tool-0.9.0}/pyproject.toml

@@ -33,14 +33,14 @@ dependencies = [
     "biocommons.seqrepo",
     "pydantic == 2.*",
     "ga4gh.vrs ~= 2.0.0a10",
-    "wags-tails ~= 0.1.3",
+    "wags-tails ~= 0.2.2",
     "bioutils",
 ]
 dynamic = ["version"]
 
 [project.optional-dependencies]
 dev = ["pre-commit>=3.7.1", "ipython", "ipykernel", "psycopg2-binary", "ruff==0.5.0"]
-test = ["pytest", "pytest-cov", "pytest-asyncio==0.18.3", "mock"]
+tests = ["pytest", "pytest-cov", "pytest-asyncio==0.18.3", "mock"]
 docs = [
     "sphinx==6.1.3",
     "sphinx-autodoc-typehints==1.22.0",

{cool_seq_tool-0.8.0 → cool_seq_tool-0.9.0}/src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -1169,14 +1169,32 @@ class ExonGenomicCoordsMapper:
         :param end: Genomic coordinate of breakpoint
         :return: Exon number corresponding to adjacent exon. Will be 0-based
         """
-        for i in range(len(tx_exons_genomic_coords) - 1):
+        # If a transcript has only one exon, return 0
+        if len(tx_exons_genomic_coords) == 1:
+            return 0
+
+        # Check if a breakpoint occurs before/after the transcript boundaries
+        bp = start if start else end
+        exon_list_len = len(tx_exons_genomic_coords) - 1
+
+        if strand == Strand.POSITIVE:
+            if bp < tx_exons_genomic_coords[0].alt_start_i:
+                return 0
+            if bp > tx_exons_genomic_coords[exon_list_len].alt_end_i:
+                return exon_list_len
+        if strand == Strand.NEGATIVE:
+            if bp > tx_exons_genomic_coords[0].alt_end_i:
+                return 0
+            if bp < tx_exons_genomic_coords[exon_list_len].alt_start_i:
+                return exon_list_len
+
+        for i in range(exon_list_len):
             exon = tx_exons_genomic_coords[i]
             if start == exon.alt_start_i:
                 break
             if end == exon.alt_end_i:
                 break
             next_exon = tx_exons_genomic_coords[i + 1]
-            bp = start if start else end
             if strand == Strand.POSITIVE:
                 lte_exon = exon
                 gte_exon = next_exon
@@ -1185,6 +1203,7 @@ class ExonGenomicCoordsMapper:
                 gte_exon = exon
             if bp >= lte_exon.alt_end_i and bp <= gte_exon.alt_start_i:
                 break
+
         # Return current exon if end position is provided, next exon if start position
         # is provided.
         return exon.ord if end else exon.ord + 1

{cool_seq_tool-0.8.0 → cool_seq_tool-0.9.0}/src/cool_seq_tool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cool_seq_tool
-Version: 0.8.0
+Version: 0.9.0
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -53,7 +53,7 @@ Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic==2.*
 Requires-Dist: ga4gh.vrs~=2.0.0a10
-Requires-Dist: wags-tails~=0.1.3
+Requires-Dist: wags-tails~=0.2.2
 Requires-Dist: bioutils
 Provides-Extra: dev
 Requires-Dist: pre-commit>=3.7.1; extra == "dev"
@@ -61,11 +61,11 @@ Requires-Dist: ipython; extra == "dev"
 Requires-Dist: ipykernel; extra == "dev"
 Requires-Dist: psycopg2-binary; extra == "dev"
 Requires-Dist: ruff==0.5.0; extra == "dev"
-Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: pytest-cov; extra == "test"
-Requires-Dist: pytest-asyncio==0.18.3; extra == "test"
-Requires-Dist: mock; extra == "test"
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Requires-Dist: pytest-asyncio==0.18.3; extra == "tests"
+Requires-Dist: mock; extra == "tests"
 Provides-Extra: docs
 Requires-Dist: sphinx==6.1.3; extra == "docs"
 Requires-Dist: sphinx-autodoc-typehints==1.22.0; extra == "docs"
@@ -76,10 +76,10 @@ Requires-Dist: furo==2023.3.27; extra == "docs"
 Requires-Dist: sphinx-github-changelog==1.2.1; extra == "docs"
 
 <h1 align="center">
-CoolSeqTool
+Cool-Seq-Tool
 </h1>
 
-[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
+[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14007783.svg)](https://doi.org/10.5281/zenodo.14007783) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
 
 ---
 
@@ -90,18 +90,18 @@ CoolSeqTool
 ## Overview
 
 <!-- description -->
-The **CoolSeqTool** provides:
+The Common Operations On Lots-Of Sequences Tool, **Cool-Seq-Tool**, provides:
 
- - A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, [MANE transcript](https://www.ncbi.nlm.nih.gov/refseq/MANE/) descriptions, and the [Universal Transcript Archive](https://github.com/biocommons/uta)
- - Augmented access to the [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, including multiple additional methods and tools
- - Mapping tools that combine the above to support translation between references sequences, annotation layers, and MANE transcripts
+- A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, [MANE transcript](https://www.ncbi.nlm.nih.gov/refseq/MANE/) descriptions, and transcript alignment data from the [Universal Transcript Archive](https://github.com/biocommons/uta)
+- Augmented access to the [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, including multiple additional methods and tools
+- Mapping tools, including a transcript selection algorithm for selecting a representative transcript defined [here](https://coolseqtool.readthedocs.io/stable/transcript_selection.html), that combine the above to support translation between references sequences, annotation layers, and transcripts
 <!-- /description -->
 
 ---
 
 ## Install
 
-CoolSeqTool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
+Cool-Seq-Tool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
 
 ```shell
 python3 -m pip install cool-seq-tool
@@ -113,7 +113,7 @@ See the [installation instructions](https://coolseqtool.readthedocs.io/stable/in
 
 ## Usage
 
-All CoolSeqTool resources can be initialized by way of a top-level class instance:
+All Cool-Seq-Tool resources can be initialized by way of a top-level class instance:
 
 ```pycon
 >>> from cool_seq_tool import CoolSeqTool

{cool_seq_tool-0.8.0 → cool_seq_tool-0.9.0}/src/cool_seq_tool.egg-info/SOURCES.txt

@@ -9,7 +9,6 @@ pyproject.toml
 .github/ISSUE_TEMPLATE/bug-report.yaml
 .github/ISSUE_TEMPLATE/feature-request.yaml
 .github/workflows/checks.yaml
-.github/workflows/close_issue.yml
 .github/workflows/pr-priority-label.yaml
 .github/workflows/release.yml
 .github/workflows/stale.yaml

{cool_seq_tool-0.8.0 → cool_seq_tool-0.9.0}/src/cool_seq_tool.egg-info/requires.txt

@@ -7,7 +7,7 @@ hgvs
 biocommons.seqrepo
 pydantic==2.*
 ga4gh.vrs~=2.0.0a10
-wags-tails~=0.1.3
+wags-tails~=0.2.2
 bioutils
 
 [dev]
@@ -26,7 +26,7 @@ sphinxext-opengraph==0.8.2
 furo==2023.3.27
 sphinx-github-changelog==1.2.1
 
-[test]
+[tests]
 pytest
 pytest-cov
 pytest-asyncio==0.18.3

{cool_seq_tool-0.8.0 → cool_seq_tool-0.9.0}/tests/conftest.py

@@ -277,6 +277,21 @@ def nm_001105539_exons_genomic_coords():
     ]
 
 
+@pytest.fixture(scope="session")
+def mm_001005183_1_exons():
+    """Create test fixture for NM_001005183.1 exons and genomic coordinates"""
+    return [
+        _ExonCoord(
+            ord=0,
+            tx_start_i=0,
+            tx_end_i=939,
+            alt_start_i=55426253,
+            alt_end_i=55427192,
+            alt_strand=Strand.POSITIVE,
+        )
+    ]
+
+
 @pytest.fixture(scope="session")
 def tpm3_1_8_start_genomic():
     """Create test fixture for genomic data for exon 1, 8"""

{cool_seq_tool-0.8.0 → cool_seq_tool-0.9.0}/tests/mappers/test_exon_genomic_coords.py

@@ -806,7 +806,10 @@ async def test_get_start_end_exon_coords(test_egc_mapper):
 
 @pytest.mark.asyncio()
 async def test_get_adjacent_exon(
-    test_egc_mapper, nm_152263_exons_genomic_coords, nm_001105539_exons_genomic_coords
+    test_egc_mapper,
+    nm_152263_exons_genomic_coords,
+    nm_001105539_exons_genomic_coords,
+    mm_001005183_1_exons,
 ):
     """Test that get_adjacent_exon works properly"""
     resp = test_egc_mapper._get_adjacent_exon(
@@ -840,6 +843,41 @@ async def test_get_adjacent_exon(
     )
     assert resp == 4
 
+    # Check cases where breakpoint occurs in before/after transcript boundaries
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=nm_001105539_exons_genomic_coords,
+        start=80486220,
+        strand=Strand.POSITIVE,
+    )
+    assert resp == 0
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=nm_001105539_exons_genomic_coords,
+        start=80526285,
+        strand=Strand.POSITIVE,
+    )
+    assert resp == 5
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=nm_152263_exons_genomic_coords,
+        end=154192110,
+        strand=Strand.NEGATIVE,
+    )
+    assert resp == 0
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=nm_152263_exons_genomic_coords,
+        end=154161809,
+        strand=Strand.NEGATIVE,
+    )
+    assert resp == 9
+
+    # Check cases where transcript only has one exon and breakpoint does not occur
+    # exon
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=mm_001005183_1_exons,
+        start=55411058,
+        strand=Strand.POSITIVE,
+    )
+    assert resp == 0
+
 
 def test_is_exonic_breakpoint(test_egc_mapper, nm_001105539_exons_genomic_coords):
     """Test is breakpoint occurs on exon"""

cool_seq_tool-0.8.0/.github/workflows/close_issue.yml

@@ -1,18 +0,0 @@
-name: Close issues related to a merged pull request based on staging branch.
-
-on:
-  pull_request:
-    types: [closed]
-    branches:
-      - staging
-
-jobs:
-  closeIssueOnPrMergeTrigger:
-
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Closes issues related to a merged pull request.
-        uses: ldez/gha-mjolnir@v1.0.3
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

cool_seq_tool-0.8.0/README.md

@@ -1,59 +0,0 @@
-<h1 align="center">
-CoolSeqTool
-</h1>
-
-[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
-
----
-
-**[Documentation](https://coolseqtool.readthedocs.io/stable/)** · [Installation](https://coolseqtool.readthedocs.io/stable/install.html) · [Usage](https://coolseqtool.readthedocs.io/stable/usage.html) · [API reference](https://coolseqtool.readthedocs.io/stable/reference/index.html)
-
----
-
-## Overview
-
-<!-- description -->
-The **CoolSeqTool** provides:
-
- - A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, [MANE transcript](https://www.ncbi.nlm.nih.gov/refseq/MANE/) descriptions, and the [Universal Transcript Archive](https://github.com/biocommons/uta)
- - Augmented access to the [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, including multiple additional methods and tools
- - Mapping tools that combine the above to support translation between references sequences, annotation layers, and MANE transcripts
-<!-- /description -->
-
----
-
-## Install
-
-CoolSeqTool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
-
-```shell
-python3 -m pip install cool-seq-tool
-```
-
-See the [installation instructions](https://coolseqtool.readthedocs.io/stable/install.html) in the documentation for a description of dependency setup requirements.
-
----
-
-## Usage
-
-All CoolSeqTool resources can be initialized by way of a top-level class instance:
-
-```pycon
->>> from cool_seq_tool import CoolSeqTool
->>> from cool_seq_tool.schemas import AnnotationLayer, CoordinateType
->>> cst = CoolSeqTool()
->>> result = await cst.mane_transcript.get_mane_transcript(
-...     "NP_004324.2",
-...     599,
-...     AnnotationLayer.PROTEIN,
-...     coordinate_type=CoordinateType.INTER_RESIDUE,
-... )
->>> result.gene, result.refseq, result.status
-('EGFR', 'NM_005228.5', <TranscriptPriority.MANE_SELECT: 'mane_select'>)
-```
-
----
-
-## Feedback and contributing
-
-We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The [documentation](https://coolseqtool.readthedocs.io/stable/contributing.html) contains guidance for submitting feedback and contributing new code.