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GenomicMedLab · Dec 8, 2023 · 88bf925 · 88bf925
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diff --git a/cool_seq_tool/sources/mane_transcript_mappings.py b/cool_seq_tool/sources/mane_transcript_mappings.py
@@ -1,4 +1,6 @@
-"""Provide fast tabular access to MANE summary file."""
+"""Provide fast tabular access to MANE summary file. Enables retrieval of associated
+MANE transcripts for gene symbols, genomic positions, or transcript accessions.
+"""
 import logging
 from pathlib import Path
 from typing import Dict, List
@@ -30,6 +32,7 @@ def __init__(self, mane_data_path: Path = MANE_SUMMARY_PATH) -> None:
 
     def _load_mane_transcript_data(self) -> pl.DataFrame:
         """Load RefSeq MANE data file into DataFrame.
+
         :return: DataFrame containing RefSeq MANE Transcript data
         """
         return pl.read_csv(self.mane_data_path, separator="\t")

diff --git a/docs/TranscriptSelectionPriority.md b/docs/TranscriptSelectionPriority.md
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -16,6 +16,7 @@ Description here.
 
     Installation<install>
     Usage<usage>
+    Transcript Selection<transcript_selection>
     API Reference<reference/index>
     Contributing<contributing>
     License<license>
diff --git a/docs/source/reference/index.rst b/docs/source/reference/index.rst
@@ -1,3 +1,5 @@
+.. _api_reference:
+
 API Reference
 =============
 

diff --git a/docs/source/transcript_selection.rst b/docs/source/transcript_selection.rst
@@ -0,0 +1,20 @@
+Transcript Selection
+====================
+
+One of the core uses of Cool-Seq-Tool is to acquire and use consensus, representative transcripts in performing genomic analysis. Here, we describe the selection processes, programmed in the :py:class:`MANETranscript <cool_seq_tool.mappers.mane_transcript.MANETranscript>` class, for choosing the best available transcripts that are compatible with requested data.
+
+We rely heavily on transcripts annotated under the `Matched Annotation from NCBI and EMBL-EBI (MANE)` Transcripts project. For more information on the MANE project, see the `NCBI MANE page <https://www.ncbi.nlm.nih.gov/refseq/MANE/>`_.
+
+Representative transcript priority
+----------------------------------
+
+All compatible transcripts are evaluated and ordered against the below criteria. The candidate transcript which meets the earliest criterion is chosen as representative.
+
+#. 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::
+
+   We prefer the most recent version of a transcript associated with an assembly.
diff --git a/docs/source/usage.rst b/docs/source/usage.rst
@@ -16,13 +16,14 @@ A core :py:class:`CoolSeqTool <cool_seq_tool.app.CoolSeqTool>` class encapsulate
    >>> from cool_seq_tool.app import CoolSeqTool
    >>> cst = CoolSeqTool()
 
-.. _configuration:
+Descriptions and examples of functions can be found in the :ref:`API Reference <api_reference>` section.
 
 REST server
 -----------
 
-Possibly staged for deletion?
+TODO Possibly staged for deletion?
 
+.. _configuration:
 
 Environment configuration
 -------------------------
@@ -52,3 +53,5 @@ Individual classes will accept arguments upon initialization to set parameters r
 
 Schema support
 --------------
+
+Many genomic data objects produced by Cool-Seq-Tool are structured in conformance with the `Variation Representation Specification <https://vrs.ga4gh.org/en/stable/>`_, courtesy of the `VRS-Python <https://github.com/ga4gh/vrs-python>` library.