Update links to point to QC pages

This now has a generic QC page and all previous rfam-annotations link
point to it. It is a generic QC page since we now also use CPAT to
annotate.

rnacentral/portal/management/commands/create_sitemaps.py

@@ -92,7 +92,7 @@ class Command(BaseCommand):
                         'help-gene-ontology-annotations',
                         'help-genomic-mapping',
                         'help-public-database',
-                        'help-rfam-annotations',
+                        'help-qc',
                         'help-rna-target-interactions',
                         'help-scientific-advisory-board',
                         'help-secondary-structure',

rnacentral/portal/rfam_matches.py

@@ -128,7 +128,7 @@ class DomainProblem(object):
                 match_domain=model.domain,
                 model_url=model.url,
                 model_name=model.short_name,
-                help_url=reverse('help-rfam-annotations'),
+                help_url=reverse('help-qc'),
             )
         )
 

rnacentral/portal/static/js/components/sequence-search/sequence-search.module.js

@@ -47,7 +47,7 @@ var sequenceSearchController = function($scope, $http, $timeout, $location, $q,
     };
 
     $scope.help = {
-        rfam: "/help/rfam-annotations",
+        rfam: "/help/qc",
         crs: "/help/conserved-motifs",
         go: "/help/gene-ontology-annotations",
         genomeMapping: "/help/genomic-mapping"

rnacentral/portal/static/js/components/sequence/rfam/rfam.component.js

@@ -10,7 +10,7 @@ var rfam = {
         var ctrl = this;
 
         ctrl.$onInit = function() {
-            ctrl.help = "/help/rfam-annotations";
+            ctrl.help = "/help/qc";
 
             // group hits with same rfam_model_id
             ctrl.groupedHits = [];

rnacentral/portal/static/js/components/text-search/text-search-results/qc-warning-tooltip.html

@@ -6,6 +6,6 @@
     <p ng-if="warning === 'missing_match'">This sequence does not match the expected Rfam family</p>
   </span>
   <p>
-    <a href="/help/rfam-annotations" style="color: #fff">Learn more &rarr;</a>
+    <a href="/help/qc" style="color: #fff">Learn more &rarr;</a>
   </p>
 </div>

rnacentral/portal/templates/portal/docs/rfam-annotations.md → rnacentral/portal/templates/portal/docs/qc.md

 
-## What is Rfam?
-
-[Rfam](http://rfam.org) is a database of functional non-coding RNA families represented by multiple sequence alignments and consensus secondary structures. The sequence and structural information is used to build [Infernal](http://eddylab.org/infernal/) covariance models, which can be used to find new instances of RNA families and annotate genomes with non-coding RNAs.
+RNAcentral provides a variety of quality checks for all sequences. Many of these checks are based off of [Rfam](http://rfam.org). [Rfam](http://rfam.org) is a database of functional non-coding RNA families represented by multiple sequence alignments and consensus secondary structures. The sequence and structural information is used to build [Infernal](http://eddylab.org/infernal/) covariance models, which can be used to find new instances of RNA families and annotate genomes with non-coding RNAs.
 
 Every release RNAcentral annotates **all sequences** with Rfam models. Rfam classification provides additional context to sequences with few annotations and help identify **potential problems**, for example, sequences which are likely contamination.
 
-## Three types of quality control using Rfam
+In addition to Rfam based checks we also use [CPAT](https://academic.oup.com/nar/article/41/6/e74/2902455) to analyze sequences. This tool detects possible open reading frames in sequences. We analyze **all** human, fly, mouse and zebrafish sequences this way. We use CPAT version 3.0.4 with the default options.
+
+## Current types of quality control
 
 ### 1. Incomplete sequences
 
@@ -43,6 +43,17 @@ The majority of RNAcentral sequences annotated as rRNA or tRNA match the corresp
 
 Browse all sequences with missing matches by searching for [`qc_warning:"missing_rfam_match"`](/search?q=qc_warning:%22missing_rfam_match%22).
 
+### 4. Possible ORFs
+
+
+Very few sequences contain open reading frames, however, it is worth noting which do as this may the function of the ncRNA.
+
+#### Examples
+
+* [Human lncRNA](/rna/URS00008D8914/9606)
+* [Fly rRNA](/rna/URS0000745350/7227)
+* [All sequences with ORFs](/search?q=qc_warning:%22possible_orf%22)
+
 ## Why some sequences do not match any Rfam families
 
 There are several possible reasons:

rnacentral/portal/templates/portal/help/rfam-annotations.html → rnacentral/portal/templates/portal/help/qc.html

@@ -28,16 +28,16 @@ Help: Rfam annotations
 <div class="row">
   <div class="col-md-8" role="main">
 
-    <h1><i class="fa fa-map-marker"></i> Rfam annotations</h1>
+    <h1><i class="fa fa-map-marker"></i> Quality Control</h1>
 
     {% load markdown_deux_tags %}
     {% markdown %}
-      {% include  'portal/docs/rfam-annotations.md' %}
+      {% include  'portal/docs/qc.md' %}
     {% endmarkdown %}
 
     <hr>
 
-    <a class="btn btn-default btn-sm" title="Edit on GitHub" href="https://github.com/RNAcentral/rnacentral-webcode/edit/master/rnacentral/portal/templates/portal/docs/rfam-annotations.md" target="_blank"><i class="fa fa-pencil-square-o"></i> Improve this page</a>
+    <a class="btn btn-default btn-sm" title="Edit on GitHub" href="https://github.com/RNAcentral/rnacentral-webcode/edit/master/rnacentral/portal/templates/portal/docs/qc.md" target="_blank"><i class="fa fa-pencil-square-o"></i> Improve this page</a>
   </div>
 
   <div class="col-md-4">

rnacentral/portal/templates/portal/help/sidebar.html

@@ -19,7 +19,7 @@
     <strong>Functional annotations</strong>
     <li><a href="{% url 'help-genomic-mapping' %}">Genomic mapping</a></li>
     <li><a href="{% url 'help-secondary-structure' %}">Secondary structure <span class="label label-success">New<span></a></li>
-    <li><a href="{% url 'help-rfam-annotations' %}">Rfam annotations</a></li>
+    <li><a href="{% url 'help-qc' %}">QC annotations</a></li>
     <li><a href="{% url 'help-gene-ontology-annotations' %}">Gene Ontology annotations</a></li>
     <li><a href="{% url 'help-rna-target-interactions' %}">RNA-target interactions</a></li>
     <li><a href="{% url 'help-conserved-motifs' %}">Conserved RNA motifs</a></li>

rnacentral/portal/tests/test_views.py

@@ -127,7 +127,7 @@ class PortalTest(TestCase):
         self.assertEqual(response.status_code, 200)
 
     def test_help_rfam_annotations_status_code(self):
-        response = self.client.get(reverse('help-rfam-annotations'))
+        response = self.client.get(reverse('help-qc'))
         self.assertEqual(response.status_code, 200)
 
     def test_help_rna_target_interactions_status_code(self):

rnacentral/portal/urls.py

@@ -46,7 +46,7 @@ urlpatterns = [
     url(r'^help/?$', views.StaticView.as_view(), {'page': 'help/faq'}, name='help'),
     url(r'^help/browser-compatibility/?$', views.StaticView.as_view(), {'page': 'help/browser-compatibility'}, name='help-browser-compatibility'),
     url(r'^help/text-search/?$', views.StaticView.as_view(), {'page': 'help/text-search'}, name='help-text-search'),
-    url(r'^help/rfam-annotations/?$', views.StaticView.as_view(), {'page': 'help/rfam-annotations'}, name='help-rfam-annotations'),
+    url(r'^help/qc/?$', views.StaticView.as_view(), {'page': 'help/qc'}, name='help-qc'),
     url(r'^help/rna-target-interactions/?$', views.StaticView.as_view(), {'page': 'help/rna-target-interactions'}, name='help-rna-target-interactions'),
     url(r'^help/gene-ontology-annotations/?$', views.StaticView.as_view(), {'page': 'help/gene-ontology-annotations'}, name='help-gene-ontology-annotations'),
     url(r'^help/genomic-mapping/?$', views.StaticView.as_view(), {'page': 'help/genomic-mapping', 'assemblies': EnsemblAssembly.objects.filter(example_chromosome__isnull=False).all()}, name='help-genomic-mapping'),