diff --git a/src/pydna/parsers.py b/src/pydna/parsers.py
index b9e81efc..0106aad2 100644
--- a/src/pydna/parsers.py
+++ b/src/pydna/parsers.py
@@ -207,123 +207,3 @@ def parse_assembly_xml(data):
doctest.testmod(verbose=True, optionflags=doctest.ELLIPSIS)
_os.environ["pydna_cached_funcs"] = cached
-
- data = """\
-
-
- >f50 14-mer
- CCCGTACAAAGGGA
- >r50 12-mer
- CTGATGCCGCGC
- >a
- CCCGTACAAAGGGAACATCCACACTTTGGTGAATCGAAGCGCGGCATCAG
-
-
- >f49 19-mer
- GATTTCCTTTTGGATACCT
- >r49 16-mer
- AAGTCTAAGGACCACG
- >b
- GATTTCCTTTTGGATACCTGAAACAAAGCCCATCGTGGTCCTTAGACTT
-
-
- >f48 13-mer
- TCCCTACACCGAC
- >r48 16-mer
- ATGAAGCTCGTCACAT
- >c
- TCCCTACACCGACGTACGATGCAACTGTGTGGATGTGACGAGCTTCAT
-
-
- """
-
- data = """\
-
-
- >f50 14-mer
- CCCGTACAAAGGGA
- >r50 12-mer
- CTGATGCCGCGC
- >a
- CCCGTACAAAGGGAACATCCACACTTTGGTGAATCGAAGCGCGGCATCAG
-
-
- >b
- GATTTCCTTTTGGATACCTGAAACAAAGCCCATCGTGGTCCTTAGACTT
-
-
- >f48 13-mer
- TCCCTACACCGAC
- >r48 16-mer
- ATGAAGCTCGTCACAT
- >c
- TCCCTACACCGACGTACGATGCAACTGTGTGGATGTGACGAGCTTCAT
-
-
- """
-
- example = parse_assembly_xml(data)
-
- # #!/usr/bin/env python3
- # # -*- coding: utf-8 -*-
- # """
- # Created on Sat Apr 22 07:39:14 2023
-
- # @author: bjorn
- # """
-
- # import xml.dom.minidom as minidom
-
- # from lxml import etree
-
- # ng = """\
- #
- #
- #
- #
- #
- #
- #
- #
- #
- #
- #
- #
- # """
-
- # from io import StringIO
-
- # f = StringIO(ng)
- # relaxng_doc = etree.parse(f)
- # relaxng = etree.RelaxNG(relaxng_doc)
-
- # xml = StringIO("""\
- #
- # 1
- # 2
- # 3
- #
- # """)
-
- # doc = etree.parse(xml)
- # relaxng.validate(doc)
-
- # doc = minidom.parseString(xml) # or minidom.parse(filename)
- # assert doc.documentElement.tagName == "assembly"
- # root = doc.getElementsByTagName('assembly')[0] # or doc.documentElement
- # items = [n for n in root.childNodes if n.nodeType == doc.ELEMENT_NODE]
-
- # for item in items:
- # print(item.childNodes[0].data)
-
- # import xml.etree.ElementTree as ET
- # xml = """\
- #
- # 1
- # 2
- # 3
- #
- # """
- # root = ET.fromstring(xml)
- # for child in root:
- # print(child.tag, child.attrib, child.text)
diff --git a/src/pydna/utils.py b/src/pydna/utils.py
index 5768d93f..08078f87 100644
--- a/src/pydna/utils.py
+++ b/src/pydna/utils.py
@@ -43,8 +43,10 @@
def three_frame_orfs(
dna: str,
limit: int = 100,
- startcodons: tuple[str, ...] = ("ATG",),
- stopcodons: tuple[str, ...] = ("TAG", "TAA", "TGA"),
+ startcodons: tuple = ("ATG",),
+ stopcodons: tuple = ("TAG", "TAA", "TGA"),
+ # startcodons: tuple[str, ...] = ("ATG",),
+ # stopcodons: tuple[str, ...] = ("TAG", "TAA", "TGA"),
):
"""Overlapping orfs in three frames."""
# breakpoint()