Merge branch 'master' of github.com:cokelaer/bioservices

Author: cokelaer

README.rst

@@ -176,6 +176,7 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+1.10.0    * Update uniprot to use the new API (june 2022)
 1.9.0     * Update unichem to reflect new API
 1.8.4     * biomodels. Fix #208
           * KEGG: fixed #204 #202 and #203

setup.py

@@ -4,7 +4,7 @@
 
 
 _MAJOR               = 1
-_MINOR               = 9
+_MINOR               = 10
 _MICRO               = 0
 version              = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
 release              = '%d.%d' % (_MAJOR, _MINOR)

src/bioservices/apps/peptides.py

@@ -8,7 +8,6 @@ class Peptides(object):
     ::
 
         >>> p = Peptides()
-        >>> p.get_fasta_sequence("Q8IYB3")
         >>> p.get_peptide_position("Q8IYB3", "VPKPEPIPEPKEPSPE")
         189
 
@@ -25,9 +24,11 @@ def __init__(self, verbose=False):
         self.sequences = {}
 
     def get_fasta_sequence(self, uniprot_name):
-        seq = self.u.get_fasta_sequence(uniprot_name)
+        seq = self.u.get_fasta(uniprot_name)
+        seq = "".join(seq.split("\n")[1:])
         return seq
 
+
     def get_phosphosite_position(self, uniprot_name, peptide):
         if uniprot_name not in self.sequences.keys():
             seq = self.get_fasta_sequence(uniprot_name)

src/bioservices/kegg.py

@@ -1354,29 +1354,30 @@ def _parse(self, res):
                 output[key] = data
             # strip only: expecting a single line (string)
             elif key in [
-                "POSITION",
+                "ANNOTATION",
+                "CATEGORY",
+                "CLASS",
+                "COMPOSITION",
+                "CREATED",
+                "DATA_SOURCE",
+                "DEFINITION",
                 "DESCRIPTION",
                 "ENTRY",
-                "ORGANISM",
-                "CLASS",
-                "SYMBOL",
+                "EFFICACY",
+                "EQUATION",
                 "FORMULA",
                 "KEYWORDS",
-                "CATEGORY",
-                "ANNOTATION",
-                "DATA_SOURCE",
+                "HISTORY",
                 "MASS",
-                "COMPOSITION",
-                "STRUCTURE",
+                "ORGANISM",
                 "ORG_CODE",
-                "CREATED",
-                "DEFINITION",
+                "POSITION",
+                "RCLASS",
                 "KO_PATHWAY",
-                "EQUATION",
+                "SYMBOL",
+                "STRUCTURE",
                 "TYPE",
-                "RCLASS",
                 "SYSNAME",
-                "HISTORY",
                 "REL_PATHWAY",
             ]:
                 # get rid of \n