Merge branch 'dev_bjorn'

.readthedocs.yml

@@ -1,14 +1,12 @@
 version: 2
-
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
 sphinx:
    configuration: docs/conf.py
-
-build:
-  image: latest
-
 conda:
   environment: docs/rtdenv.yml
-
 python:
    install:
       - method: pip

src/pydna/dseq.py

@@ -109,22 +109,22 @@ class Dseq(_Seq):
 
     The ovhg parameter controls the stagger at the five prime end::
 
-        dsDNA    ovhg
+        dsDNA       overhang
 
-          XXX    2
-        XXXXX
+          nnn...    2
+        nnnnn...
 
-         XXXX    1
-        XXXXX
+         nnnn...    1
+        nnnnn...
 
-        XXXXX    0
-        XXXXX
+        nnnnn...    0
+        nnnnn...
 
-        XXXXX   -1
-         XXXX
+        nnnnn...   -1
+         nnnn...
 
-        XXXXX   -2
-          XXX
+        nnnnn...   -2
+          nnn...
 
     Example of creating Dseq objects with different amounts of stagger:
 

src/pydna/parsers.py

@@ -24,6 +24,7 @@
 def embl_gb_fasta(raw, ds, path=None):
     # regex = r"^>.+?^(?=$|LOCUS|ID|>|\#)|^(?:LOCUS|ID).+?^//"
     regex = r"(?:>.+\n^(?:^[^>]+?)(?=\n\n|>|" r"LOCUS|ID))|(?:(?:LOCUS|ID)(?:(?:.|\n)+?)^//)"
+    "(?:^>.+\n^(?:^[^>]+?)(?=\n\n|>|^LOCUS|ID))|(?:(?:^LOCUS|ID)(?:(?:.|\n)+?)^//)"
 
     result_list = []
 

src/pydna/utils.py

@@ -129,7 +129,7 @@ def smallest_rotation(s):
     """
     from pydivsufsort import min_rotation
 
-    k = min_rotation(s)
+    k = min_rotation(bytes(s, "ascii"))
     return s[k:] + s[:k]