Document start_codons locus attribute.

kjolley · Nov 15, 2021 · ed21e9a · ed21e9a
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diff --git a/administration.rst b/administration.rst
@@ -652,6 +652,12 @@ exclamation mark (!) next to them:
 * max_length - Maximum length of locus (optional).
 
   * Allowed: any integer (larger than the minimum length).
+
+* complete_cds - Whether locus represents a complete coding sequence (optional)
+
+* start_codons - Semi-colon separated list of alternative start codons to allow
+
+  * Note that these are in addition to the built-in defaults of ATG, GTG, TTG.
 
 * orf - Open reading frame of locus (optional). 
 
@@ -825,6 +831,12 @@ exclamation mark (!) next to them:
   false).
 
   * Allowed: any integer.
+
+* complete_cds - Whether locus represents a complete coding sequence (optional)
+
+* start_codons - Semi-colon separated list of alternative start codons to allow
+
+  * Note that these are in addition to the built-in defaults of ATG, GTG, TTG.
 
 * orf - Open reading frame of locus (optional). 1-3 are the forward reading 
   frame, 4-6 are the reverse reading frames.

diff --git a/dbase_setup.rst b/dbase_setup.rst
@@ -634,6 +634,13 @@ Any value set here can be overridden in a
   * Force the use of a specific set when accessing database via this XML
     configuration: Value is the name of the set. 
 
+* start_codons
+
+  * Semi-colon separated list of start codons to allow. Note that this list
+    will replace the built-in defaults of ATG, GTG, and TTG, and is used for
+    all functions that require recognising complete coding sequences, such as
+    automated allele definition.
+
 * start_id
 
   * Defines the minimum record id to be used when uploading new isolate 
@@ -1147,6 +1154,12 @@ Any value set here can be overridden in a
   * Force the use of a specific set when accessing database via this XML
     configuration: Value is the name of the set.
 
+* start_codons
+
+  * Semi-colon separated list of start codons to allow. Note that this list
+    will replace the built-in defaults of ATG, GTG, and TTG, and is used for
+    all functions that require recognising complete coding sequences.
+
 * submissions
 
   * Enable automated submission system: either 'yes' or 'no', default 'no'