update docs with example of alternative start codon use

widdowquinn · Jul 21, 2022 · c0f7962 · c0f7962
1 parent e92a7f9
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diff --git a/docs/examples.rst b/docs/examples.rst
@@ -18,6 +18,20 @@ The command below [#f1]_ identifies coding sequences from NCBI format
         tests/examples/ncbi [email protected] -v
 
 
+----------------------------------------
+NCBI format input sequences - no introns
+----------------------------------------
+
+The command below [#f1]_ identifies coding sequences from NCBI format
+[#f2]_ input for two proteins, one of which has an alternative start
+site. 
+
+.. code-block:: bash
+
+    ncfp --allow_alternative_start_codon \
+		tests/test_input/sequences/input_alternative_start.fasta \
+		tests/examples/alternative_start [email protected] -v
+
 -------------------------------------------
 UniProt format input sequences - no introns
 -------------------------------------------

diff --git a/docs/licensing.rst b/docs/licensing.rst
@@ -7,7 +7,7 @@ Licensing
 Unless otherwise indicated, all code is subject to the following agreement:
 
   (c) The James Hutton Institute 2017-2019
-  (c) The University of Strathclyde 2019-2020
+  (c) The University of Strathclyde 2019-2022
   Author: Leighton Pritchard
 
   Contact: [email protected]
@@ -26,7 +26,7 @@ The MIT License
 ---------------
 
 Copyright (c) 2017-2019 The James Hutton Institute
-Copyright (c) 2019-2020 The University of Strathclyde
+Copyright (c) 2019-2022 The University of Strathclyde
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in the

diff --git a/docs/requirements.rst b/docs/requirements.rst
@@ -13,7 +13,7 @@ Python
     - Python version 3.5 or higher
 
 Python Packages
-    - `biopython`_
+    - `biopython`_ (must be v1.10 or higher due to UniProt API changes)
     - `bioservices`_
     - `tqdm`_