docs: use correct app name + update transcript selection algorithm

README.md

@@ -1,5 +1,5 @@
 <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)
@@ -13,18 +13,18 @@ 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
@@ -36,7 +36,7 @@ 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

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:

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.

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