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()