From b147467690f07cc54794c612e95596b3b5502dd3 Mon Sep 17 00:00:00 2001 From: Kori Kuzma Date: Mon, 25 Nov 2024 19:13:42 -0500 Subject: [PATCH] docs: use correct app name (Cool-Seq-Tool) + update transcript selection algorithm --- README.md | 14 +++++++------- docs/source/index.rst | 8 ++++---- docs/source/transcript_selection.rst | 7 ++++--- docs/source/usage.rst | 2 +- 4 files changed, 16 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index 526cdde9..51641050 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@

-CoolSeqTool +Cool-Seq-Tool

[![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 -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 --- ## 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 diff --git a/docs/source/index.rst b/docs/source/index.rst index f9ef8e36..092bbb8f 100644 --- a/docs/source/index.rst +++ b/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 `_ descriptions, and the `Universal Transcript Archive `_ +* A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, `MANE transcript `_ descriptions, and transcript alignment data from the `Universal Transcript Archive `_ * Augmented access to the `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 `, that combine the above to support translation between various references sequences and annotation layers, and transcripts See the :ref:`Installation ` and :ref:`Usage ` pages for information on getting started. Individual classes and methods are documented within the :ref:`API reference `. -CoolSeqTool was created to support the `Knowledgebase Integration Project `_ of the `Variant Interpretation for Cancer Consortium (VICC) `_. It is developed primarily by the `Wagner Lab `_. Full source code is available on `GitHub `_. +Cool-Seq-Tool was created to support the `Knowledgebase Integration Project `_ of the `Variant Interpretation for Cancer Consortium (VICC) `_. It is developed primarily by the `Wagner Lab `_. Full source code is available on `GitHub `_. .. toctree:: :hidden: diff --git a/docs/source/transcript_selection.rst b/docs/source/transcript_selection.rst index 48630af5..c8e7c891 100644 --- a/docs/source/transcript_selection.rst +++ b/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. diff --git a/docs/source/usage.rst b/docs/source/usage.rst index e1fa423e..161a5711 100644 --- a/docs/source/usage.rst +++ b/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 `, :py:class:`ExonGenomicCoordsMapper `, and :py:class:`ManeTranscript `, 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 `, :py:class:`ExonGenomicCoordsMapper `, and :py:class:`ManeTranscript `, define public methods as ``async``. This means that, when used inside another function, they must be called with ``await``: .. code-block:: python