%global _empty_manifest_terminate_build 0 Name: python-pydna Version: 5.2.0 Release: 1 Summary: Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules. License: BSD URL: https://pypi.org/project/pydna/ Source0: https://mirrors.nju.edu.cn/pypi/web/packages/84/da/0c926cecd9ea436f54b9ec2e3aa8ab6f71936ce5eb8be312db68ec0ce5a0/pydna-5.2.0.tar.gz BuildArch: noarch Requires: python3-appdirs Requires: python3-biopython Requires: python3-cai2 Requires: python3-matplotlib Requires: python3-networkx Requires: python3-pillow Requires: python3-prettytable Requires: python3-pyfiglet Requires: python3-pyparsing Requires: python3-pyperclip Requires: python3-pyqt5 Requires: python3-requests Requires: python3-scipy %description # ![icon](https://raw.githubusercontent.com/bjornFJohansson/pydna/master/docs/pics/pydna.resized.png) pydna | [![Tests & Coverage](https://github.com/BjornFJohansson/pydna/workflows/Tests%20&%20Coverage/badge.svg)](https://github.com/BjornFJohansson/pydna/actions?query=workflow%3A%22Tests+%26+Coverage%22) |[![codecov](https://codecov.io/gh/BjornFJohansson/pydna/branch/master/graph/badge.svg)](https://codecov.io/gh/BjornFJohansson/pydna/branch/master) | [![PyPI version](https://badge.fury.io/py/pydna.svg)](https://badge.fury.io/py/pydna) |[![Anaconda-Server Badge](https://anaconda.org/bjornfjohansson/pydna/badges/version.svg)](https://anaconda.org/bjornfjohansson/pydna) | [![Google group : pydna](https://img.shields.io/badge/Google%20Group-pydna-blue.svg)](https://groups.google.com/g/pydna) | |---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------| | [![Documentation Status](https://readthedocs.org/projects/pydna/badge/?version=latest)](http://pydna.readthedocs.io/?badge=latest) |[![GitHub issues](https://img.shields.io/github/issues/BjornFJohansson/pydna.svg)](https://github.com/BjornFJohansson/pydna/issues) | [![Anaconda-Server Badge2](https://anaconda.org/bjornfjohansson/pydna/badges/license.svg)](https://anaconda.org/bjornfjohansson/pydna) |[![GitHub stars](https://img.shields.io/github/stars/BjornFJohansson/pydna.svg)](https://github.com/BjornFJohansson/pydna/stargazers) | | Planning genetic constructs with many parts and assembly steps, such as recombinant metabolic pathways :petri_dish:, are often difficult to **properly** document as is evident from the poor state of documentation in the scientific literature :radioactive:. The pydna python package provide a human-readable formal descriptions of :dna: cloning and genetic assembly strategies in Python :snake: which allow for simulation and verification. Pydna can be used as [executable documentation](https://en.wikipedia.org/wiki/Literate_programming) for cloning. A cloning strategy expressed in pydna is **complete**, **unambiguous** and **stable**. Pydna provides simulation of: - Restriction digestion - Ligation - PCR - Primer design - Gibson assembly - Golden gate assembly - Homologous recombination - Gel electrophoresis of DNA with generation of gel images Virtually any sub-cloning experiment can be described in pydna, and its execution yield the sequences of intermediate and final DNA molecules. Pydna has been designed with the goal of being understandable for biologists with only some basic understanding of Python. Pydna can formalize planning and sharing of cloning strategies and is especially useful for complex or combinatorial DNA molecule constructions. To get started, we have compiled some [simple examples](https://github.com/MetabolicEngineeringGroupCBMA/pydna-examples#pydna-examples). For more elaborate use, look at some assembly strategies of D-xylose metabolic pathways [MetabolicEngineeringGroupCBMA/ypk-xylose-pathways](https://github.com/MetabolicEngineeringGroupCBMA/ypk-xylose-pathways#pereira-et-al-2016). ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Usage Most pydna functionality is implemented as methods for the double stranded DNA sequence record classes Dseq and Dseqrecord, which are subclasses of the [Biopython](http://biopython.org/wiki/Main_Page) [Seq](http://biopython.org/wiki/Seq) and [SeqRecord](http://biopython.org/wiki/SeqRecord) classes. These classes make cut and paste cloning and PCR very simple: >>> from pydna.dseq import Dseq >>> seq = Dseq("GGATCCAAA","TTTGGATCC",ovhg=0) >>> seq Dseq(-9) GGATCCAAA CCTAGGTTT >>> from Bio.Restriction import BamHI >>> a,b = seq.cut(BamHI) >>> a Dseq(-5) G CCTAG >>> b Dseq(-8) GATCCAAA GTTT >>> a+b Dseq(-9) GGATCCAAA CCTAGGTTT >>> b+a Dseq(-13) GATCCAAAG GTTTCCTAG >>> b+a+b Dseq(-17) GATCCAAAGGATCCAAA GTTTCCTAGGTTT >>> b+a+a Traceback (most recent call last): File "", line 1, in File "/usr/local/lib/python2.7/dist-packages/pydna/dsdna.py", line 217, in __add__ raise TypeError("sticky ends not compatible!") TypeError: sticky ends not compatible! >>> As the example above shows, pydna keeps track of sticky ends. Notably, homologous recombination and Gibson assembly between linear DNA fragments can be easily simulated without any additional information besides the primary sequence of the fragments. Gel electrophoresis of DNA fragments can be simulated using the included gel module Jupyter QtConsole 4.7.7 Python 3.8.5 | packaged by conda-forge | (default, Aug 29 2020, 01:22:49) Type 'copyright', 'credits' or 'license' for more information IPython 7.18.1 -- An enhanced Interactive Python. Type '?' for help. In [1]: from pydna.gel import gel In [2]: from pydna.ladders import PennStateLadder In [3]: from pydna.dseqrecord import Dseqrecord In [4]: gel([PennStateLadder,[Dseqrecord("A"*2000)]]) Out[4]: ![](https://raw.githubusercontent.com/BjornFJohansson/pydna/master/scripts/pydna_gel.png) Pydna can be very compact. The eleven lines of Python below simulates the construction of a recombinant plasmid. DNA sequences are downloaded from Genbank by accession numbers that are guaranteed to be stable over time. from pydna.genbank import Genbank gb = Genbank("myself@email.com") # Tell Genbank who you are! gene = gb.nucleotide("X06997") # Kluyveromyces lactis LAC12 gene for lactose permease. from pydna.parsers import parse_primers primer_f,primer_r = parse_primers(''' >760_KlLAC12_rv (20-mer) ttaaacagattctgcctctg >759_KlLAC12_fw (19-mer) aaatggcagatcattcgag ''') from pydna.amplify import pcr pcr_prod = pcr(primer_f,primer_r, gene) vector = gb.nucleotide("AJ001614") # pCAPs cloning vector from Bio.Restriction import EcoRV lin_vector = vector.linearize(EcoRV) rec_vec = ( lin_vector + pcr_prod ).looped() Pydna can automate the simulation of [sub cloning](http://en.wikipedia.org/wiki/Subcloning) experiments using python. This is helpful to generate examples for teaching purposes. Read the documentation (below) or the [cookbook](https://github.com/BjornFJohansson/pydna/blob/master/docs/cookbook/cookbook.ipynb) with example files for further information. Please post a message in the [google group](https://groups.google.com/d/forum/pydna) for pydna if you need help or have problems, questions or comments :sos:. Feedback & suggestions are very welcome! ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Who is using pydna? Taylor, L. J., & Strebel, K. (2017). Pyviko: an automated Python tool to design gene knockouts in complex viruses with overlapping genes. BMC Microbiology, 17(1), 12. [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/28061810) Wang, Y., Xue, H., Pourcel, C., Du, Y., & Gautheret, D. (2021). 2-kupl: mapping-free variant detection from DNA-seq data of matched samples. In Cold Spring Harbor Laboratory (p. 2021.01.17.427048). [DOI](https://doi.org/10.1101/2021.01.17.427048) [PubMed](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8180056) [An Automated Protein Synthesis Pipeline with Transcriptic and Snakemake](http://blog.booleanbiotech.com/transcriptic_protein_synthesis_pipeline.html) and other projects on [github](https://github.com/BjornFJohansson/pydna/network/dependents?package_id=UGFja2FnZS01MjQ2MjYzNQ%3D%3D) ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) There is an open access paper in BMC Bioinformatics describing pydna: [![abstr](https://raw.githubusercontent.com/bjornFJohansson/pydna/master/docs/pics/BMC_resized.png)](http://www.biomedcentral.com/1471-2105/16/142/abstract) Please reference the above paper: Pereira, F., Azevedo, F., Carvalho, Â., Ribeiro, G. F., Budde, M. W., & Johansson, B. (2015). Pydna: a simulation and documentation tool for DNA assembly strategies using python. BMC Bioinformatics, 16(142), 142. When using pydna. ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Documentation Documentation is built using [Sphinx](http://www.sphinx-doc.org/) from [docstrings](https://www.python.org/dev/peps/pep-0257/) in the code and displayed at readthedocs [![Documentation Status](https://readthedocs.org/projects/pydna/badge/?version=latest)](http://pydna.readthedocs.io/?badge=latest) The [numpy](www.numpy.org) [docstring format](https://github.com/numpy/numpy/blob/release/doc/HOWTO_DOCUMENT.rst.txt) is used. ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Installation using pip Pip is included in recent Python versions and is the officially [recommended](http://python-packaging-user-guide.readthedocs.org/en/latest) tool. Pip installs the minimal installation requirements automatically, but not the optional requirements (see below). pip install pydna or use the --pre switch to get the latest version of pydna. pip install pydna --pre for optional functionality do: pip install pydna[gel,download,express,gui] Remove options inside the square brackets as required, but be sure not to leave spaces as pip will not recognize the options. See below under "Optional dependencies". ### Windows: You should be able to pip install pydna from the Windows terminal as biopython now can be installed with pip as well. C:\> pip install pydna By default python and pip are not on the PATH. You can re-install Python and select this option during installation, or give the full path for pip. Try something like this, depending on where your copy of Python is installed: C:\Python37\Scripts\pip install pydna ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Source Code Pydna is developed on [Github](https://github.com/BjornFJohansson/pydna) :octocat:. ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Minimal installation dependencies Pydna versions before 1.0.0 were compatible with python 2.7 only. The list below is the minimal requirements for installing pydna. Biopython has c-extensions, but the other modules are pure python. - [Python 3.8, 3.9, 3.10 or 3.11](http://www.python.org) - [appdirs >=1.4.4](https://pypi.python.org/pypi/appdirs) - [biopython >= 1.80](http://pypi.python.org/pypi/biopython) - [networkx >=2.8.8](http://pypi.python.org/pypi/networkx) - [prettytable >=3.5.0](https://pypi.python.org/pypi/PrettyTable) - [pyperclip >=1.8.2](https://pypi.python.org/pypi/PrettyTable) - [pyfiglet >=0.8.post1](https://pypi.python.org/pypi/PrettyTable) ## Optional dependencies If the modules listed below in the first column are installed, they will provide the functionality listed in the second column. | Dependency | Function in pydna | |-------------------------------------------------------------|--------------------------------------------------------| | [scipy >=1.8.0](https://www.scipy.org) | gel simulation with pydna.gel | | [matplotlib >=3.4.3](http://matplotlib.org) | “ | | [pillow >=8.4.0](https://github.com/python-pillow/Pillow) | “ | | [numpy](http://www.numpy.org) | " | | [pyparsing >=2.4.7](https://pypi.python.org/pypi/pyparsing) | fix corrupt Genbank files with pydna.genbankfixer | | [requests >=2.26.0](https://pypi.org/project/requests) | download sequences with pydna.download | | [cai2 >=1.0.5](https://pypi.python.org/pypi/cai2) | codon adaptation index calculations in several modules | | [pyqt5 >=5.15.0](https://pypi.python.org/pypi/pyqt5) | codon adaptation index calculations in several modules | ## Requirements for running tests and analyzing code coverage - [pytest](https://pypi.org/project/pytest) - [pytest-cov](https://pypi.org/project/pytest-cov) - [pytest-doctestplus](https://pypi.org/project/pytest-doctestplus) - [coverage](https://pypi.org/project/coverage) - [nbval](https://pypi.org/project/nbval) - [requests-mock](https://pypi.org/project/requests-mock) ![----](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Releases See the [releases](https://github.com/BjornFJohansson/pydna/releases) for changes and releases. ![----](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Automatic testing & Release process There are three github actions associated with this package: - `pydna_test_and_coverage_workflow.yml` The `pydna_test_and_coverage_workflow.yml` is triggered on all pushed non-tagged commits. This workflow run tests, doctests and a series of Jupyter notebooks using pytest. The two other workflows build a setuptools wheel and packages for different Python versions on Linux, Windows and macOS. These are triggered by publishing a github release manually from the github interface. ![----](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Building a PyPI package with [Poetry](https://pypi.org/project/poetry) 1. Commit changes to git 2. Tag the commit according to the [Semantic Versioning](https://semver.org) format, for example "v2.0.1a3". Do not forget the "v" or poetry will not recognize the tag. git tag v2.0.1a3 3. Pydna uses the poetry [poetry-dynamic-versioning](https://pypi.org/project/poetry-dynamic-versioning) plugin. poetry dynamic-versioning # This sets the version number in the source files 4. Verify the version poetry version 5. Build package: poetry build # run this command in the root directory where the pyproject.toml file is located 6. Verify the filename of the files in the dist/ folder, they should match 7. Publish to pypi poetry publish ![----](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## History Pydna was made public in 2012 on [Google code](https://code.google.com/archive/p/pydna). :microbe: :portugal: %package -n python3-pydna Summary: Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules. Provides: python-pydna BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-pydna # ![icon](https://raw.githubusercontent.com/bjornFJohansson/pydna/master/docs/pics/pydna.resized.png) pydna | [![Tests & Coverage](https://github.com/BjornFJohansson/pydna/workflows/Tests%20&%20Coverage/badge.svg)](https://github.com/BjornFJohansson/pydna/actions?query=workflow%3A%22Tests+%26+Coverage%22) |[![codecov](https://codecov.io/gh/BjornFJohansson/pydna/branch/master/graph/badge.svg)](https://codecov.io/gh/BjornFJohansson/pydna/branch/master) | [![PyPI version](https://badge.fury.io/py/pydna.svg)](https://badge.fury.io/py/pydna) |[![Anaconda-Server Badge](https://anaconda.org/bjornfjohansson/pydna/badges/version.svg)](https://anaconda.org/bjornfjohansson/pydna) | [![Google group : pydna](https://img.shields.io/badge/Google%20Group-pydna-blue.svg)](https://groups.google.com/g/pydna) | |---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------| | [![Documentation Status](https://readthedocs.org/projects/pydna/badge/?version=latest)](http://pydna.readthedocs.io/?badge=latest) |[![GitHub issues](https://img.shields.io/github/issues/BjornFJohansson/pydna.svg)](https://github.com/BjornFJohansson/pydna/issues) | [![Anaconda-Server Badge2](https://anaconda.org/bjornfjohansson/pydna/badges/license.svg)](https://anaconda.org/bjornfjohansson/pydna) |[![GitHub stars](https://img.shields.io/github/stars/BjornFJohansson/pydna.svg)](https://github.com/BjornFJohansson/pydna/stargazers) | | Planning genetic constructs with many parts and assembly steps, such as recombinant metabolic pathways :petri_dish:, are often difficult to **properly** document as is evident from the poor state of documentation in the scientific literature :radioactive:. The pydna python package provide a human-readable formal descriptions of :dna: cloning and genetic assembly strategies in Python :snake: which allow for simulation and verification. Pydna can be used as [executable documentation](https://en.wikipedia.org/wiki/Literate_programming) for cloning. A cloning strategy expressed in pydna is **complete**, **unambiguous** and **stable**. Pydna provides simulation of: - Restriction digestion - Ligation - PCR - Primer design - Gibson assembly - Golden gate assembly - Homologous recombination - Gel electrophoresis of DNA with generation of gel images Virtually any sub-cloning experiment can be described in pydna, and its execution yield the sequences of intermediate and final DNA molecules. Pydna has been designed with the goal of being understandable for biologists with only some basic understanding of Python. Pydna can formalize planning and sharing of cloning strategies and is especially useful for complex or combinatorial DNA molecule constructions. To get started, we have compiled some [simple examples](https://github.com/MetabolicEngineeringGroupCBMA/pydna-examples#pydna-examples). For more elaborate use, look at some assembly strategies of D-xylose metabolic pathways [MetabolicEngineeringGroupCBMA/ypk-xylose-pathways](https://github.com/MetabolicEngineeringGroupCBMA/ypk-xylose-pathways#pereira-et-al-2016). ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Usage Most pydna functionality is implemented as methods for the double stranded DNA sequence record classes Dseq and Dseqrecord, which are subclasses of the [Biopython](http://biopython.org/wiki/Main_Page) [Seq](http://biopython.org/wiki/Seq) and [SeqRecord](http://biopython.org/wiki/SeqRecord) classes. These classes make cut and paste cloning and PCR very simple: >>> from pydna.dseq import Dseq >>> seq = Dseq("GGATCCAAA","TTTGGATCC",ovhg=0) >>> seq Dseq(-9) GGATCCAAA CCTAGGTTT >>> from Bio.Restriction import BamHI >>> a,b = seq.cut(BamHI) >>> a Dseq(-5) G CCTAG >>> b Dseq(-8) GATCCAAA GTTT >>> a+b Dseq(-9) GGATCCAAA CCTAGGTTT >>> b+a Dseq(-13) GATCCAAAG GTTTCCTAG >>> b+a+b Dseq(-17) GATCCAAAGGATCCAAA GTTTCCTAGGTTT >>> b+a+a Traceback (most recent call last): File "", line 1, in File "/usr/local/lib/python2.7/dist-packages/pydna/dsdna.py", line 217, in __add__ raise TypeError("sticky ends not compatible!") TypeError: sticky ends not compatible! >>> As the example above shows, pydna keeps track of sticky ends. Notably, homologous recombination and Gibson assembly between linear DNA fragments can be easily simulated without any additional information besides the primary sequence of the fragments. Gel electrophoresis of DNA fragments can be simulated using the included gel module Jupyter QtConsole 4.7.7 Python 3.8.5 | packaged by conda-forge | (default, Aug 29 2020, 01:22:49) Type 'copyright', 'credits' or 'license' for more information IPython 7.18.1 -- An enhanced Interactive Python. Type '?' for help. In [1]: from pydna.gel import gel In [2]: from pydna.ladders import PennStateLadder In [3]: from pydna.dseqrecord import Dseqrecord In [4]: gel([PennStateLadder,[Dseqrecord("A"*2000)]]) Out[4]: ![](https://raw.githubusercontent.com/BjornFJohansson/pydna/master/scripts/pydna_gel.png) Pydna can be very compact. The eleven lines of Python below simulates the construction of a recombinant plasmid. DNA sequences are downloaded from Genbank by accession numbers that are guaranteed to be stable over time. from pydna.genbank import Genbank gb = Genbank("myself@email.com") # Tell Genbank who you are! gene = gb.nucleotide("X06997") # Kluyveromyces lactis LAC12 gene for lactose permease. from pydna.parsers import parse_primers primer_f,primer_r = parse_primers(''' >760_KlLAC12_rv (20-mer) ttaaacagattctgcctctg >759_KlLAC12_fw (19-mer) aaatggcagatcattcgag ''') from pydna.amplify import pcr pcr_prod = pcr(primer_f,primer_r, gene) vector = gb.nucleotide("AJ001614") # pCAPs cloning vector from Bio.Restriction import EcoRV lin_vector = vector.linearize(EcoRV) rec_vec = ( lin_vector + pcr_prod ).looped() Pydna can automate the simulation of [sub cloning](http://en.wikipedia.org/wiki/Subcloning) experiments using python. This is helpful to generate examples for teaching purposes. Read the documentation (below) or the [cookbook](https://github.com/BjornFJohansson/pydna/blob/master/docs/cookbook/cookbook.ipynb) with example files for further information. Please post a message in the [google group](https://groups.google.com/d/forum/pydna) for pydna if you need help or have problems, questions or comments :sos:. Feedback & suggestions are very welcome! ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Who is using pydna? Taylor, L. J., & Strebel, K. (2017). Pyviko: an automated Python tool to design gene knockouts in complex viruses with overlapping genes. BMC Microbiology, 17(1), 12. [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/28061810) Wang, Y., Xue, H., Pourcel, C., Du, Y., & Gautheret, D. (2021). 2-kupl: mapping-free variant detection from DNA-seq data of matched samples. In Cold Spring Harbor Laboratory (p. 2021.01.17.427048). [DOI](https://doi.org/10.1101/2021.01.17.427048) [PubMed](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8180056) [An Automated Protein Synthesis Pipeline with Transcriptic and Snakemake](http://blog.booleanbiotech.com/transcriptic_protein_synthesis_pipeline.html) and other projects on [github](https://github.com/BjornFJohansson/pydna/network/dependents?package_id=UGFja2FnZS01MjQ2MjYzNQ%3D%3D) ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) There is an open access paper in BMC Bioinformatics describing pydna: [![abstr](https://raw.githubusercontent.com/bjornFJohansson/pydna/master/docs/pics/BMC_resized.png)](http://www.biomedcentral.com/1471-2105/16/142/abstract) Please reference the above paper: Pereira, F., Azevedo, F., Carvalho, Â., Ribeiro, G. F., Budde, M. W., & Johansson, B. (2015). Pydna: a simulation and documentation tool for DNA assembly strategies using python. BMC Bioinformatics, 16(142), 142. When using pydna. ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Documentation Documentation is built using [Sphinx](http://www.sphinx-doc.org/) from [docstrings](https://www.python.org/dev/peps/pep-0257/) in the code and displayed at readthedocs [![Documentation Status](https://readthedocs.org/projects/pydna/badge/?version=latest)](http://pydna.readthedocs.io/?badge=latest) The [numpy](www.numpy.org) [docstring format](https://github.com/numpy/numpy/blob/release/doc/HOWTO_DOCUMENT.rst.txt) is used. ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Installation using pip Pip is included in recent Python versions and is the officially [recommended](http://python-packaging-user-guide.readthedocs.org/en/latest) tool. Pip installs the minimal installation requirements automatically, but not the optional requirements (see below). pip install pydna or use the --pre switch to get the latest version of pydna. pip install pydna --pre for optional functionality do: pip install pydna[gel,download,express,gui] Remove options inside the square brackets as required, but be sure not to leave spaces as pip will not recognize the options. See below under "Optional dependencies". ### Windows: You should be able to pip install pydna from the Windows terminal as biopython now can be installed with pip as well. C:\> pip install pydna By default python and pip are not on the PATH. You can re-install Python and select this option during installation, or give the full path for pip. Try something like this, depending on where your copy of Python is installed: C:\Python37\Scripts\pip install pydna ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Source Code Pydna is developed on [Github](https://github.com/BjornFJohansson/pydna) :octocat:. ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Minimal installation dependencies Pydna versions before 1.0.0 were compatible with python 2.7 only. The list below is the minimal requirements for installing pydna. Biopython has c-extensions, but the other modules are pure python. - [Python 3.8, 3.9, 3.10 or 3.11](http://www.python.org) - [appdirs >=1.4.4](https://pypi.python.org/pypi/appdirs) - [biopython >= 1.80](http://pypi.python.org/pypi/biopython) - [networkx >=2.8.8](http://pypi.python.org/pypi/networkx) - [prettytable >=3.5.0](https://pypi.python.org/pypi/PrettyTable) - [pyperclip >=1.8.2](https://pypi.python.org/pypi/PrettyTable) - [pyfiglet >=0.8.post1](https://pypi.python.org/pypi/PrettyTable) ## Optional dependencies If the modules listed below in the first column are installed, they will provide the functionality listed in the second column. | Dependency | Function in pydna | |-------------------------------------------------------------|--------------------------------------------------------| | [scipy >=1.8.0](https://www.scipy.org) | gel simulation with pydna.gel | | [matplotlib >=3.4.3](http://matplotlib.org) | “ | | [pillow >=8.4.0](https://github.com/python-pillow/Pillow) | “ | | [numpy](http://www.numpy.org) | " | | [pyparsing >=2.4.7](https://pypi.python.org/pypi/pyparsing) | fix corrupt Genbank files with pydna.genbankfixer | | [requests >=2.26.0](https://pypi.org/project/requests) | download sequences with pydna.download | | [cai2 >=1.0.5](https://pypi.python.org/pypi/cai2) | codon adaptation index calculations in several modules | | [pyqt5 >=5.15.0](https://pypi.python.org/pypi/pyqt5) | codon adaptation index calculations in several modules | ## Requirements for running tests and analyzing code coverage - [pytest](https://pypi.org/project/pytest) - [pytest-cov](https://pypi.org/project/pytest-cov) - [pytest-doctestplus](https://pypi.org/project/pytest-doctestplus) - [coverage](https://pypi.org/project/coverage) - [nbval](https://pypi.org/project/nbval) - [requests-mock](https://pypi.org/project/requests-mock) ![----](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Releases See the [releases](https://github.com/BjornFJohansson/pydna/releases) for changes and releases. ![----](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Automatic testing & Release process There are three github actions associated with this package: - `pydna_test_and_coverage_workflow.yml` The `pydna_test_and_coverage_workflow.yml` is triggered on all pushed non-tagged commits. This workflow run tests, doctests and a series of Jupyter notebooks using pytest. The two other workflows build a setuptools wheel and packages for different Python versions on Linux, Windows and macOS. These are triggered by publishing a github release manually from the github interface. ![----](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Building a PyPI package with [Poetry](https://pypi.org/project/poetry) 1. Commit changes to git 2. Tag the commit according to the [Semantic Versioning](https://semver.org) format, for example "v2.0.1a3". Do not forget the "v" or poetry will not recognize the tag. git tag v2.0.1a3 3. Pydna uses the poetry [poetry-dynamic-versioning](https://pypi.org/project/poetry-dynamic-versioning) plugin. poetry dynamic-versioning # This sets the version number in the source files 4. Verify the version poetry version 5. Build package: poetry build # run this command in the root directory where the pyproject.toml file is located 6. Verify the filename of the files in the dist/ folder, they should match 7. Publish to pypi poetry publish ![----](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## History Pydna was made public in 2012 on [Google code](https://code.google.com/archive/p/pydna). :microbe: :portugal: %package help Summary: Development documents and examples for pydna Provides: python3-pydna-doc %description help # ![icon](https://raw.githubusercontent.com/bjornFJohansson/pydna/master/docs/pics/pydna.resized.png) pydna | [![Tests & Coverage](https://github.com/BjornFJohansson/pydna/workflows/Tests%20&%20Coverage/badge.svg)](https://github.com/BjornFJohansson/pydna/actions?query=workflow%3A%22Tests+%26+Coverage%22) |[![codecov](https://codecov.io/gh/BjornFJohansson/pydna/branch/master/graph/badge.svg)](https://codecov.io/gh/BjornFJohansson/pydna/branch/master) | [![PyPI version](https://badge.fury.io/py/pydna.svg)](https://badge.fury.io/py/pydna) |[![Anaconda-Server Badge](https://anaconda.org/bjornfjohansson/pydna/badges/version.svg)](https://anaconda.org/bjornfjohansson/pydna) | [![Google group : pydna](https://img.shields.io/badge/Google%20Group-pydna-blue.svg)](https://groups.google.com/g/pydna) | |---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------| | [![Documentation Status](https://readthedocs.org/projects/pydna/badge/?version=latest)](http://pydna.readthedocs.io/?badge=latest) |[![GitHub issues](https://img.shields.io/github/issues/BjornFJohansson/pydna.svg)](https://github.com/BjornFJohansson/pydna/issues) | [![Anaconda-Server Badge2](https://anaconda.org/bjornfjohansson/pydna/badges/license.svg)](https://anaconda.org/bjornfjohansson/pydna) |[![GitHub stars](https://img.shields.io/github/stars/BjornFJohansson/pydna.svg)](https://github.com/BjornFJohansson/pydna/stargazers) | | Planning genetic constructs with many parts and assembly steps, such as recombinant metabolic pathways :petri_dish:, are often difficult to **properly** document as is evident from the poor state of documentation in the scientific literature :radioactive:. The pydna python package provide a human-readable formal descriptions of :dna: cloning and genetic assembly strategies in Python :snake: which allow for simulation and verification. Pydna can be used as [executable documentation](https://en.wikipedia.org/wiki/Literate_programming) for cloning. A cloning strategy expressed in pydna is **complete**, **unambiguous** and **stable**. Pydna provides simulation of: - Restriction digestion - Ligation - PCR - Primer design - Gibson assembly - Golden gate assembly - Homologous recombination - Gel electrophoresis of DNA with generation of gel images Virtually any sub-cloning experiment can be described in pydna, and its execution yield the sequences of intermediate and final DNA molecules. Pydna has been designed with the goal of being understandable for biologists with only some basic understanding of Python. Pydna can formalize planning and sharing of cloning strategies and is especially useful for complex or combinatorial DNA molecule constructions. To get started, we have compiled some [simple examples](https://github.com/MetabolicEngineeringGroupCBMA/pydna-examples#pydna-examples). For more elaborate use, look at some assembly strategies of D-xylose metabolic pathways [MetabolicEngineeringGroupCBMA/ypk-xylose-pathways](https://github.com/MetabolicEngineeringGroupCBMA/ypk-xylose-pathways#pereira-et-al-2016). ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Usage Most pydna functionality is implemented as methods for the double stranded DNA sequence record classes Dseq and Dseqrecord, which are subclasses of the [Biopython](http://biopython.org/wiki/Main_Page) [Seq](http://biopython.org/wiki/Seq) and [SeqRecord](http://biopython.org/wiki/SeqRecord) classes. These classes make cut and paste cloning and PCR very simple: >>> from pydna.dseq import Dseq >>> seq = Dseq("GGATCCAAA","TTTGGATCC",ovhg=0) >>> seq Dseq(-9) GGATCCAAA CCTAGGTTT >>> from Bio.Restriction import BamHI >>> a,b = seq.cut(BamHI) >>> a Dseq(-5) G CCTAG >>> b Dseq(-8) GATCCAAA GTTT >>> a+b Dseq(-9) GGATCCAAA CCTAGGTTT >>> b+a Dseq(-13) GATCCAAAG GTTTCCTAG >>> b+a+b Dseq(-17) GATCCAAAGGATCCAAA GTTTCCTAGGTTT >>> b+a+a Traceback (most recent call last): File "", line 1, in File "/usr/local/lib/python2.7/dist-packages/pydna/dsdna.py", line 217, in __add__ raise TypeError("sticky ends not compatible!") TypeError: sticky ends not compatible! >>> As the example above shows, pydna keeps track of sticky ends. Notably, homologous recombination and Gibson assembly between linear DNA fragments can be easily simulated without any additional information besides the primary sequence of the fragments. Gel electrophoresis of DNA fragments can be simulated using the included gel module Jupyter QtConsole 4.7.7 Python 3.8.5 | packaged by conda-forge | (default, Aug 29 2020, 01:22:49) Type 'copyright', 'credits' or 'license' for more information IPython 7.18.1 -- An enhanced Interactive Python. Type '?' for help. In [1]: from pydna.gel import gel In [2]: from pydna.ladders import PennStateLadder In [3]: from pydna.dseqrecord import Dseqrecord In [4]: gel([PennStateLadder,[Dseqrecord("A"*2000)]]) Out[4]: ![](https://raw.githubusercontent.com/BjornFJohansson/pydna/master/scripts/pydna_gel.png) Pydna can be very compact. The eleven lines of Python below simulates the construction of a recombinant plasmid. DNA sequences are downloaded from Genbank by accession numbers that are guaranteed to be stable over time. from pydna.genbank import Genbank gb = Genbank("myself@email.com") # Tell Genbank who you are! gene = gb.nucleotide("X06997") # Kluyveromyces lactis LAC12 gene for lactose permease. from pydna.parsers import parse_primers primer_f,primer_r = parse_primers(''' >760_KlLAC12_rv (20-mer) ttaaacagattctgcctctg >759_KlLAC12_fw (19-mer) aaatggcagatcattcgag ''') from pydna.amplify import pcr pcr_prod = pcr(primer_f,primer_r, gene) vector = gb.nucleotide("AJ001614") # pCAPs cloning vector from Bio.Restriction import EcoRV lin_vector = vector.linearize(EcoRV) rec_vec = ( lin_vector + pcr_prod ).looped() Pydna can automate the simulation of [sub cloning](http://en.wikipedia.org/wiki/Subcloning) experiments using python. This is helpful to generate examples for teaching purposes. Read the documentation (below) or the [cookbook](https://github.com/BjornFJohansson/pydna/blob/master/docs/cookbook/cookbook.ipynb) with example files for further information. Please post a message in the [google group](https://groups.google.com/d/forum/pydna) for pydna if you need help or have problems, questions or comments :sos:. Feedback & suggestions are very welcome! ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Who is using pydna? Taylor, L. J., & Strebel, K. (2017). Pyviko: an automated Python tool to design gene knockouts in complex viruses with overlapping genes. BMC Microbiology, 17(1), 12. [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/28061810) Wang, Y., Xue, H., Pourcel, C., Du, Y., & Gautheret, D. (2021). 2-kupl: mapping-free variant detection from DNA-seq data of matched samples. In Cold Spring Harbor Laboratory (p. 2021.01.17.427048). [DOI](https://doi.org/10.1101/2021.01.17.427048) [PubMed](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8180056) [An Automated Protein Synthesis Pipeline with Transcriptic and Snakemake](http://blog.booleanbiotech.com/transcriptic_protein_synthesis_pipeline.html) and other projects on [github](https://github.com/BjornFJohansson/pydna/network/dependents?package_id=UGFja2FnZS01MjQ2MjYzNQ%3D%3D) ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) There is an open access paper in BMC Bioinformatics describing pydna: [![abstr](https://raw.githubusercontent.com/bjornFJohansson/pydna/master/docs/pics/BMC_resized.png)](http://www.biomedcentral.com/1471-2105/16/142/abstract) Please reference the above paper: Pereira, F., Azevedo, F., Carvalho, Â., Ribeiro, G. F., Budde, M. W., & Johansson, B. (2015). Pydna: a simulation and documentation tool for DNA assembly strategies using python. BMC Bioinformatics, 16(142), 142. When using pydna. ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Documentation Documentation is built using [Sphinx](http://www.sphinx-doc.org/) from [docstrings](https://www.python.org/dev/peps/pep-0257/) in the code and displayed at readthedocs [![Documentation Status](https://readthedocs.org/projects/pydna/badge/?version=latest)](http://pydna.readthedocs.io/?badge=latest) The [numpy](www.numpy.org) [docstring format](https://github.com/numpy/numpy/blob/release/doc/HOWTO_DOCUMENT.rst.txt) is used. ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Installation using pip Pip is included in recent Python versions and is the officially [recommended](http://python-packaging-user-guide.readthedocs.org/en/latest) tool. Pip installs the minimal installation requirements automatically, but not the optional requirements (see below). pip install pydna or use the --pre switch to get the latest version of pydna. pip install pydna --pre for optional functionality do: pip install pydna[gel,download,express,gui] Remove options inside the square brackets as required, but be sure not to leave spaces as pip will not recognize the options. See below under "Optional dependencies". ### Windows: You should be able to pip install pydna from the Windows terminal as biopython now can be installed with pip as well. C:\> pip install pydna By default python and pip are not on the PATH. You can re-install Python and select this option during installation, or give the full path for pip. Try something like this, depending on where your copy of Python is installed: C:\Python37\Scripts\pip install pydna ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Source Code Pydna is developed on [Github](https://github.com/BjornFJohansson/pydna) :octocat:. ![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Minimal installation dependencies Pydna versions before 1.0.0 were compatible with python 2.7 only. The list below is the minimal requirements for installing pydna. Biopython has c-extensions, but the other modules are pure python. - [Python 3.8, 3.9, 3.10 or 3.11](http://www.python.org) - [appdirs >=1.4.4](https://pypi.python.org/pypi/appdirs) - [biopython >= 1.80](http://pypi.python.org/pypi/biopython) - [networkx >=2.8.8](http://pypi.python.org/pypi/networkx) - [prettytable >=3.5.0](https://pypi.python.org/pypi/PrettyTable) - [pyperclip >=1.8.2](https://pypi.python.org/pypi/PrettyTable) - [pyfiglet >=0.8.post1](https://pypi.python.org/pypi/PrettyTable) ## Optional dependencies If the modules listed below in the first column are installed, they will provide the functionality listed in the second column. | Dependency | Function in pydna | |-------------------------------------------------------------|--------------------------------------------------------| | [scipy >=1.8.0](https://www.scipy.org) | gel simulation with pydna.gel | | [matplotlib >=3.4.3](http://matplotlib.org) | “ | | [pillow >=8.4.0](https://github.com/python-pillow/Pillow) | “ | | [numpy](http://www.numpy.org) | " | | [pyparsing >=2.4.7](https://pypi.python.org/pypi/pyparsing) | fix corrupt Genbank files with pydna.genbankfixer | | [requests >=2.26.0](https://pypi.org/project/requests) | download sequences with pydna.download | | [cai2 >=1.0.5](https://pypi.python.org/pypi/cai2) | codon adaptation index calculations in several modules | | [pyqt5 >=5.15.0](https://pypi.python.org/pypi/pyqt5) | codon adaptation index calculations in several modules | ## Requirements for running tests and analyzing code coverage - [pytest](https://pypi.org/project/pytest) - [pytest-cov](https://pypi.org/project/pytest-cov) - [pytest-doctestplus](https://pypi.org/project/pytest-doctestplus) - [coverage](https://pypi.org/project/coverage) - [nbval](https://pypi.org/project/nbval) - [requests-mock](https://pypi.org/project/requests-mock) ![----](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Releases See the [releases](https://github.com/BjornFJohansson/pydna/releases) for changes and releases. ![----](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Automatic testing & Release process There are three github actions associated with this package: - `pydna_test_and_coverage_workflow.yml` The `pydna_test_and_coverage_workflow.yml` is triggered on all pushed non-tagged commits. This workflow run tests, doctests and a series of Jupyter notebooks using pytest. The two other workflows build a setuptools wheel and packages for different Python versions on Linux, Windows and macOS. These are triggered by publishing a github release manually from the github interface. ![----](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## Building a PyPI package with [Poetry](https://pypi.org/project/poetry) 1. Commit changes to git 2. Tag the commit according to the [Semantic Versioning](https://semver.org) format, for example "v2.0.1a3". Do not forget the "v" or poetry will not recognize the tag. git tag v2.0.1a3 3. Pydna uses the poetry [poetry-dynamic-versioning](https://pypi.org/project/poetry-dynamic-versioning) plugin. poetry dynamic-versioning # This sets the version number in the source files 4. Verify the version poetry version 5. Build package: poetry build # run this command in the root directory where the pyproject.toml file is located 6. Verify the filename of the files in the dist/ folder, they should match 7. Publish to pypi poetry publish ![----](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/colored.png) ## History Pydna was made public in 2012 on [Google code](https://code.google.com/archive/p/pydna). :microbe: :portugal: %prep %autosetup -n pydna-5.2.0 %build %py3_build %install %py3_install install -d -m755 %{buildroot}/%{_pkgdocdir} if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi pushd %{buildroot} if [ -d usr/lib ]; then find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/lib64 ]; then find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/bin ]; then find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/sbin ]; then find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst fi touch doclist.lst if [ -d usr/share/man ]; then find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst fi popd mv %{buildroot}/filelist.lst . mv %{buildroot}/doclist.lst . %files -n python3-pydna -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Wed May 10 2023 Python_Bot - 5.2.0-1 - Package Spec generated