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pydna-group · Mar 27, 2024 · a805598 · a805598
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Showing 2 changed files with 4 additions and 122 deletions.
diff --git 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 = """\
-    <assembly topology="circular">
-    <amplicon>
-    >f50 14-mer
-    CCCGTACAAAGGGA
-    >r50 12-mer
-    CTGATGCCGCGC
-    >a
-    CCCGTACAAAGGGAACATCCACACTTTGGTGAATCGAAGCGCGGCATCAG
-    </amplicon>
-    <amplicon>
-    >f49 19-mer
-    GATTTCCTTTTGGATACCT
-    >r49 16-mer
-    AAGTCTAAGGACCACG
-    >b
-    GATTTCCTTTTGGATACCTGAAACAAAGCCCATCGTGGTCCTTAGACTT
-    </amplicon>
-    <amplicon>
-    >f48 13-mer
-    TCCCTACACCGAC
-    >r48 16-mer
-    ATGAAGCTCGTCACAT
-    >c
-    TCCCTACACCGACGTACGATGCAACTGTGTGGATGTGACGAGCTTCAT
-    </amplicon>
-    </assembly>
-    """
-
-    data = """\
-    <assembly topology="circular">
-    <amplicon>
-    >f50 14-mer
-    CCCGTACAAAGGGA
-    >r50 12-mer
-    CTGATGCCGCGC
-    >a
-    CCCGTACAAAGGGAACATCCACACTTTGGTGAATCGAAGCGCGGCATCAG
-    </amplicon>
-    <fragment>
-    >b
-    GATTTCCTTTTGGATACCTGAAACAAAGCCCATCGTGGTCCTTAGACTT
-    </fragment>
-    <amplicon>
-    >f48 13-mer
-    TCCCTACACCGAC
-    >r48 16-mer
-    ATGAAGCTCGTCACAT
-    >c
-    TCCCTACACCGACGTACGATGCAACTGTGTGGATGTGACGAGCTTCAT
-    </amplicon>
-    </assembly>
-    """
-
-    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 = """\
-    # <element name="assembly" xmlns="http://relaxng.org/ns/structure/1.0">
-    #   <zeroOrMore>
-    #     <interleave>
-    #         <element name="amplicon">
-    #             <text/>
-    #         </element>
-    #         <element name="fragment">
-    #             <text/>
-    #         </element>
-    #     </interleave>
-    #   </zeroOrMore>
-    # </element>
-    # """
-
-    # from io import StringIO
-
-    # f = StringIO(ng)
-    # relaxng_doc = etree.parse(f)
-    # relaxng = etree.RelaxNG(relaxng_doc)
-
-    # xml = StringIO("""\
-    # <assembly topology="circular">
-    # <amplicon>1</amplicon>
-    # <fragment>2</fragment>
-    # <amplicon>3</amplicon>
-    # </assembly>
-    # """)
-
-    # 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 = """\
-    # <assembly topology="circular">
-    # <amplicon>1</amplicon>
-    # <fragment>2</fragment>
-    # <amplicon>3</amplicon>
-    # </assembly>
-    # """
-    # 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
@@ -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()