Update KEGG documentation fixes #233

cokelaer · Oct 1, 2022 · 73058b1 · 73058b1
1 parent 104d1fe
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Showing 5 changed files with 21 additions and 3 deletions.
diff --git a/README.rst b/README.rst
@@ -13,11 +13,12 @@ BIOSERVICES: access to biological web services programmatically
     :target: http://bioservices.readthedocs.org/en/main/?badge=main
     :alt: Documentation Status
 
+.. image:: https://static.pepy.tech/personalized-badge/bioservices?period=month&units=international_system&left_color=black&right_color=orange&left_text=Downloads
+    :target: https://pepy.tech/project/bioservices
+
 .. image:: https://raw.githubusercontent.com/cokelaer/bioservices/main/doc/_static/bioservices2_logo_256.png
     :target: https://raw.githubusercontent.com/cokelaer/bioservices/main/doc/_static/bioservices2_logo_256.png
 
-.. image:: https://static.pepy.tech/personalized-badge/bioservices?period=month&units=international_system&left_color=black&right_color=orange&left_text=Downloads
-    :target: https://pepy.tech/project/bioservices
 
 :Python_version_available: BioServices is tested for Python 3.7, 3.8, 3.9
 :Contributions: Please join https://github.com/cokelaer/bioservices 
@@ -192,6 +193,7 @@ Version   Description
 ========= ====================================================================
 1.10.3    * Update pdb service to use v2 API
           * remove biocarta (website not accesible anymore)
+          * Update Chembl (no API changes)
 1.10.2    * Fix #226 and applied PR from Fix from @GianArauz
             https://github.com/cokelaer/bioservices/pull/232 about UniProt 
             error

diff --git a/doc/index.rst b/doc/index.rst
@@ -62,5 +62,4 @@ User guide
     references
     external_references.rst
     faqs
-    ChangeLog.rst
     contributors
diff --git a/src/bioservices/kegg.py b/src/bioservices/kegg.py
@@ -542,6 +542,10 @@ def get(self, dbentries, option=None, parse=False):
               # same as above
               s.get("hsa05130", "image")
 
+              # to retrieve genome, you must preceed the entry with gn:
+              s.get('gn:T01001')
+              # to retrieve a network, you must preceed it with network:
+              s.get('network:nt06214')
 
           Another example here below shows how to save the image of a given pathway::
 
@@ -1366,6 +1370,7 @@ def _parse(self, res):
                 "KEYWORDS",
                 "HISTORY",
                 "MASS",
+                "MAP",
                 "ORGANISM",
                 "ORG_CODE",
                 "POSITION",
@@ -1455,6 +1460,7 @@ def _parse(self, res):
                 "COMPOUND",
                 "RMODULE",
                 "PATHWAY_MAP",
+                "MEMBER",
                 "STR_MAP",
                 "OTHER_MAP",
                 "PATHWAY",

diff --git a/src/bioservices/uniprot.py b/src/bioservices/uniprot.py
@@ -771,6 +771,15 @@ def get_df(self, entries, nChunk=100, organism=None, limit=10):
             set it to None to keep all entries but this will be very slow
         :return: dataframe with indices being the uniprot id (e.g. DIG1_YEAST)
 
+        To get about 100 columns related to the accession P62988, type:
+
+            df = u.get_df('P62988')
+
+        Note that you may preceed the accesion by the keyword **sec_acc) to access secondary 
+        accessions numbers::
+
+            df = u.get_df('sec_acc:P62988')
+
         """
         if isinstance(entries, str):
             entries = [entries]

diff --git a/test/webservices/test_kegg.py b/test/webservices/test_kegg.py
@@ -159,6 +159,8 @@ def test_get(kegg):
         assert False
     except:
         assert True
+    res = kegg.get('network:nt06214')
+
 
 
 def test_parse(kegg, parse_input):