Add more work

cool_seq_tool/data/data_downloads.py

@@ -25,7 +25,7 @@ def __init__(self) -> None:
 
     def get_mane_summary(self) -> Path:
         """Identify latest MANE summary data. If unavailable locally, download from
-        source.
+        `NCBI FTP server <https://ftp.ncbi.nlm.nih.gov/refseq/MANE/MANE_human/current/>`_.
 
         :return: path to MANE summary file
         """
@@ -52,7 +52,7 @@ def get_mane_summary(self) -> Path:
 
     def get_lrg_refseq_gene_data(self) -> Path:
         """Identify latest LRG RefSeq Gene file. If unavailable locally, download from
-        source.
+        `NCBI FTP server <https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/>`_.
 
         :return: path to acquired LRG RefSeq Gene data file
         """

docs/source/index.rst

@@ -15,7 +15,6 @@ Description here.
    :maxdepth: 2
 
     Installation<install>
-    Overview<overview>
     Usage<usage>
     API Reference<reference/index>
     Contributing<contributing>

docs/source/usage.rst

@@ -1,15 +1,54 @@
 Usage
 =====
 
-.. _configuration:
+Cool-Seq-Tool provides easy access to, and useful operations on, a selection of important genomic resources. Modules are divided into three groups:
+
+* :ref:`Data sources <sources_modules_api_index>`, for basic acquisition and setup for a data source via Python
+
+* :ref:`Data handlers <handlers_modules_api_index>`, for additional operations on top of existing sources
+
+* :ref:`Data mappers <mappers_modules_api_index>`, for functions that incorporate multiple sources/handlers to produce output
 
-Configuration
--------------
+A core :py:class:`CoolSeqTool <cool_seq_tool.app.CoolSeqTool>` class encapsulates all of their functions and can be used for easy initialization:
 
-Programmatic access
--------------------
+.. code-block:: pycon
+
+   >>> from cool_seq_tool.app import CoolSeqTool
+   >>> cst = CoolSeqTool()
+
+.. _configuration:
 
 REST server
 -----------
 
 Possibly staged for deletion?
+
+
+Environment configuration
+-------------------------
+
+Individual classes will accept arguments upon initialization to set parameters regarding data sources. In general, these parameters are also configurable via environment variables, e.g. in a cloud deployment.
+
+.. list-table::
+   :widths: 25 100
+   :header-rows: 1
+
+   * - Variable
+     - Description
+   * - ``LRG_REFSEQGENE_PATH``
+     - Path to LRG_RefSeqGene file. Used in :py:class:`TranscriptMappings <cool_seq_tool.sources.transcript_mappings.TranscriptMappings>` to provide mappings between gene symbols and RefSeq/Ensembl transcript accessions. If not defined, defaults to the most recent version (formatted as ``data/LRG_RefSeqGene_YYYYMMDD``) within the Cool-Seq-Tool library directory.
+   * - ``TRANSCRIPT_MAPPINGS_PATH``
+     - Path to transcript mapping file generated from `Ensembl BioMart <http://www.ensembl.org/biomart/martview>`_. Used in :py:class:`TranscriptMappings <cool_seq_tool.sources.transcript_mappings.TranscriptMappings>`. If not defined, uses a copy of the file that is bundled within the Cool-Seq-Tool installation. See the :ref:`contributor instructions <build_transcript_mappings_tsv>` for information on manually rebuilding it.
+   * - ``MANE_SUMMARY_PATH``
+     - Path to MANE Summary file. Used in :py:class:`MANETranscriptMappings <cool_seq_tool.sources.mane_transcript_mappings.MANETranscriptMappings>` to provide MANE transcript annotations. If not defined, defaults to the most recent version (formatted as ``data/MANE.GRCh38vX.X.summary.txt``) within the Cool-Seq-Tool library directory.
+   * - ``SEQREPO_ROOT_DIR``
+     - Path to SeqRepo directory (i.e. contains ``aliases.sqlite3`` database file, and ``sequences`` directory). Used by :py:class:`SeqRepoAccess <cool_seq_tool.handlers.seqrepo_access.SeqRepoAccess`. If not defined, defaults to ``/usr/local/share/seqrepo/latest``.
+   * - ``UTA_DB_URL``
+     - A `libpq connection string <https://www.postgresql.org/docs/current/libpq-connect.html#LIBPQ-CONNSTRING>`_, i.e. of the form ``postgresql://<user>:<password>@<host>:<port>/<database>/<schema>``, used by the :py:class:`cool_seq_tool.sources.uta_database.UTADatabase` class. By default, it is set to ``postgresql://uta_admin:uta@localhost:5433/uta/uta_20210129b``.
+   * - ``LIFTOVER_CHAIN_37_TO_38``
+     - A path to a `chainfile <https://genome.ucsc.edu/goldenPath/help/chain.html>`_ for lifting from GRCh37 to GRCh38. Used by :py:class:`cool_seq_tool.sources.uta_database.UTADatabase` as input to `pyliftover <https://pypi.org/project/pyliftover/>`_. If not provided, pyliftover will fetch it automatically from UCSC.
+   * - ``LIFTOVER_CHAIN_38_TO_37``
+     - A path to a `chainfile <https://genome.ucsc.edu/goldenPath/help/chain.html>`_ for lifting from GRCh38 to GRCh37. Used by :py:class:`cool_seq_tool.sources.uta_database.UTADatabase` as input to `pyliftover <https://pypi.org/project/pyliftover/>`_. If not provided, pyliftover will fetch it automatically from UCSC.
+
+Schema support
+--------------