Merge pull request #221 from cokelaer/june_2022_cleanup

Fix peptides.py to reflect new uniprot api
cokelaer · Jul 1, 2022 · 12dca31 · 12dca31
2 parents 84d2eb2 + 5b3160f
commit 12dca31
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diff --git a/src/bioservices/apps/peptides.py b/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)

diff --git a/test/test_apps_peptides.py b/test/test_apps_peptides.py
@@ -6,5 +6,4 @@ def test_peptides():
     p = Peptides()
     pos = p.get_phosphosite_position("Q8IYB3", "VPKPEPIPEPKEPSPE")
     assert pos == [740, 901]
-    p.get_fasta_sequence("Q8IYB3")