Merge pull request #105 from metagenlab/nj/fix_pfam

Fix Pfam identifiers
metagenlab · Jul 2, 2024 · 1310d82 · 1310d82
2 parents 1f60493 + ff93703
commit 1310d82
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diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
@@ -64,6 +64,7 @@ to [Common Changelog](https://common-changelog.org)
 
 ### Fixed
 
+- Fix PFAM identifiers missing leading 0. ([#105](https://github.com/metagenlab/zDB/pull/105)) (Niklaus Johner)
 - Fix product representation in GWAS view for orthogroups. ([#102](https://github.com/metagenlab/zDB/pull/102)) (Niklaus Johner)
 - Fix Scoary-2 integration. ([#101](https://github.com/metagenlab/zDB/pull/101)) (Niklaus Johner)
 - Fix search_bar results view when all loci miss any gene annotation. ([#99](https://github.com/metagenlab/zDB/pull/99)) (Niklaus Johner)

diff --git a/webapp/templates/chlamdb/fam.html b/webapp/templates/chlamdb/fam.html
@@ -84,7 +84,7 @@ <h3 class="panel-title">Description</h3>
                       {% if object_type == 'pfam' %}
                         <tr>
                           <th>External link</th>
-                          <td><a href="http://pfam.xfam.org/family/{{ fam }}" target="_blank"> {{ fam }} <i class="fas fa-external-link-alt"></i></a></td>
+                          <td><a href="https://www.ebi.ac.uk/interpro/entry/pfam/{{ fam }}" target="_blank"> {{ fam }} <i class="fas fa-external-link-alt"></i></a></td>
                         </tr>
 
                       {% elif object_type == 'interpro' %}

diff --git a/webapp/templates/chlamdb/home.html b/webapp/templates/chlamdb/home.html
@@ -290,7 +290,7 @@ <h3 class="title">{{metadata.group_metadata.object_name_plural}}</h3>
                                 <dd> - <a href="https://www.ncbi.nlm.nih.gov/COG/" target="_blank">COG</a> (clusters of orthologous groups, reference DB version {{versions|keyvalue:"CDD"}})</dd>
                               {% endif %}
                               {% if optional2status|keyvalue:"pfam" == 1 %}
-                                <dd> - <a href="http://pfam.xfam.org" target="_blank" >Pfam</a> (protein families, reference DB version {{versions|keyvalue:"Pfam"}})</dd>
+                                <dd> - <a href="https://interpro-documentation.readthedocs.io/en/latest/pfam.html" target="_blank" >Pfam</a> (protein families, reference DB version {{versions|keyvalue:"Pfam"}})</dd>
                               {% endif %}
                               {% if optional2status|keyvalue:"KEGG" == 1 %}
                                 <dd> - <a href="https://www.genome.jp/kegg/" target="_blank" >KEGG</a> (Kegg orthologs, reference DB version {{versions|keyvalue:"Ko"}})</dd>
@@ -321,7 +321,7 @@ <h3 class="title">{{metadata.group_metadata.object_name_plural}}</h3>
                                   <dd> -<a href="https://www.ncbi.nlm.nih.gov/COG/" target="_blank">COG</a> (clusters of orthologous groups)</dd>
                                 {% endif %}
                                 {% if not optional2status|keyvalue:"pfam" == 1 %}
-                                  <dd> - <a href="http://pfam.xfam.org" target="_blank">Pfam</a> (protein families)</dd>
+                                  <dd> - <a href="https://interpro-documentation.readthedocs.io/en/latest/pfam.html" target="_blank">Pfam</a> (protein families)</dd>
                                 {% endif %}
                                 {% if not optional2status|keyvalue:"KEGG" == 1 %}
                                   <dd> - <a href="https://www.genome.jp/kegg/" target="_blank" >KEGG</a> (Kegg orthologs)</dd>

diff --git a/webapp/views/utils.py b/webapp/views/utils.py
@@ -144,7 +144,7 @@ def format_hmm_url(hmm_id):
 
 def format_pfam(pfam_id, base=None, to_url=False):
     if base is None:
-        fmt_entry = f"PF{pfam_id:04d}"
+        fmt_entry = f"PF{pfam_id:05d}"
     else:
         fmt_entry = base
     if to_url: