removed pins

cgat/IndexedFasta.py

@@ -901,15 +901,15 @@ def getSequence(self,
 
         if self.mNoSeek:
             # read directly from position
-            p.fromstring(
+            p.frombytes(
                 self.mDatabaseFile.read(block_size, data[3],
                                         first_pos, last_pos))
         else:
             first_pos += pos_seq
             last_pos += pos_seq
 
             self.mDatabaseFile.seek(first_pos)
-            p.fromstring(self.mDatabaseFile.read(last_pos - first_pos))
+            p.frombytes(self.mDatabaseFile.read(last_pos - first_pos))
 
         if str(strand) in ("-", "0", "-1"):
             p = AString(Genomics.reverse_complement(str(p)))

cgat/SequenceProperties.py

@@ -141,7 +141,7 @@ def loadSequence(self, sequence, seqtype="na"):
         # map to printable letters: hid has length 22, so the padded '=' are
         # truncated. You have to add them, if you ever want to decode,
         # but who would do such a thing :=)
-        r = base64.encodestring(h)[0:22].decode("ascii")
+        r = base64.encodebytes(h)[0:22].decode("ascii")
 
         # finally substitute some characters:
         # '/' for '_', so we have legal file names

conda/environments/cgat-apps.yml

@@ -26,7 +26,6 @@ dependencies:
 - pybigwig
 - pysam>=0.18.0
 - pyyaml
-- pytest<=5.4.3
 - quicksect
 - rdflib
 - scikit-learn