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| [![Tests & Coverage](https://github.com/BjornFJohansson/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml/badge.svg?branch=dev_bjorn)](https://github.com/BjornFJohansson/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml) | [![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) | [![Google group : pydna](https://img.shields.io/badge/Google%20Group-pydna-blue.svg)](https://groups.google.com/g/pydna) |
| -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------- |
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Expand All @@ -12,7 +12,8 @@ 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.
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**.
Expand Down Expand Up @@ -40,7 +41,7 @@ DNA molecule constructions.

Start by looking at the [cookbook](https://github.com/BjornFJohansson/pydna/blob/master/docs/cookbook/cookbook.ipynb).

Some simple examples can be found [here](https://github.com/MetabolicEngineeringGroupCBMA/pydna-examples#pydna-examples).
Some simple examples can be found [here](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).

Expand All @@ -53,7 +54,8 @@ See below for documentation.
## 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.
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 PCR primer design, PCR simulation and cut-and-paste cloning very simple:

Expand Down Expand Up @@ -81,7 +83,7 @@ DNA sequences are downloaded from Genbank by accession numbers that are guarante
lin_vector = vector.linearize(EcoRV)
rec_vec = ( lin_vector + pcr_prod ).looped()

Another use case for pydna in the automatic generation of [sub cloning](http://en.wikipedia.org/wiki/Subcloning) examples for teaching purposes. These examples
Another use case for pydna in the automatic generation of [sub cloning](http://en.wikipedia.org/wiki/Subcloning) examples for teaching purposes.

Feedback & suggestions are very welcome! 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:.

Expand All @@ -104,7 +106,6 @@ In Cold Spring Harbor Laboratory (p. 2021.01.17.427048). [DOI](https://doi.org/1

[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)

![----]( http://bit.ly/coloredline)
Expand All @@ -115,19 +116,21 @@ There is an open access paper in BMC Bioinformatics describing pydna:

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.

![----]( http://bit.ly/coloredline)

## Documentation :page_with_curl:

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.
Documentation can be found [here](https://bjornfjohansson.github.io/pydna). It is built using [Sphinx](http://www.sphinx-doc.org/) from [docstrings](https://www.python.org/dev/peps/pep-0257/)
using a GitHub [action](https://github.com/BjornFJohansson/pydna/actions/workflows/publish-docs.yml).
The [numpy](www.numpy.org) [docstring format](https://numpy.org/doc/stable/dev/howto-docs.html#docstring-intro) is used.





![----]( http://bit.ly/coloredline)

Expand Down Expand Up @@ -165,40 +168,6 @@ By default python and pip are not on the PATH. You can re-install Python and sel
Pydna is developed on [Github](https://github.com/BjornFJohansson/pydna) :octocat:.
I am happy to collaborate on new features or bugfixes.

We use [pre-commit-hooks](https://github.com/pre-commit/pre-commit-hooks) to help with source code formatting.
Prior to each commit, a series of checks and source code formatters are run (see `.pre-commit-config.yaml` file below).
This can modify the commited code, which might have to be added again.

A good practice is to run `pre-commit run --all-files` before committing.

The `.pre-commit-config.yaml` file located in the root of the repository has the following content:


```
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.5.0
hooks:
- id: no-commit-to-branch
args: [--branch, master]
- id: check-yaml
- id: end-of-file-fixer
- id: trailing-whitespace
- id: debug-statements
- id: fix-encoding-pragma
- id: mixed-line-ending
- repo: https://github.com/ambv/black
rev: 24.2.0
hooks:
- id: black
- repo: https://github.com/PyCQA/flake8
rev: 7.0.0
hooks:
- id: flake8
exclude: scripts/|docs/|tests/
```


## Minimal installation dependencies

The list below is the minimal requirements for installing pydna.
Expand Down Expand Up @@ -228,30 +197,31 @@ Enables the `pydna.dseqrecord.Dseqrecord.copy_gb_to_clipboard()` and `pydna.dseq
These methods will put a copy the sequence on the clipboard in either Genbank (gb) or fasta format.


| Dependency | Function in pydna |
| --------------------------------------------------- | ------------------------------------------------------ |
| [pyperclip](https://pypi.python.org/pypi/pyperclip) | copy sequence to clipboard |
| Dependency | Function in pydna |
| --------------------------------------------------- | -------------------------------------- |
| [pyperclip](https://pypi.python.org/pypi/pyperclip) | copy sequence to clipboard |

### download
### `download`

Pyparsing enables the `pydna.genbankfixer.gbtext_clean()` function that can automatically
correct malformed sequence files in Genbank format. These are often found online, so this option also installs requests to enable the `pydna.genbankfixer.download.download_text()` function which can be used to get cleaned up text from a URL.
correct malformed sequence files in Genbank format. These are often found online, so this
option also installs requests to enable the `pydna.genbankfixer.download.download_text()` function which can be used to get cleaned up text from a URL.


| Dependency | Function in pydna |
| --------------------------------------------------- | ------------------------------------------------------ |
| [pyparsing](https://pypi.python.org/pypi/pyparsing) | fix corrupt Genbank files with pydna.genbankfixer |
| [requests](https://pypi.org/project/requests) | download sequences with pydna.download |

### express
### `express`

This option enables the `pydna.utils.cai()` function and the `cai()` method
available from subclasses of `pydna.seqrecord.SeqRecord`, such as
`pydna.dseqrecord.Dseqrecord`.

| [cai2](https://pypi.python.org/pypi/cai2) | codon adaptation index calculations in several modules |

### gel
### `gel`

Scipy, matplotlib and pillow (PIL) enable the generation of gel images. Numpy is also
needed, but usually installed as a dependency of biopython.
Expand Down

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