semvec/pypi-packages huggingface dataset:
biostats 0.0.1
Bio tools addons
License: MIT

# biostats

This tool was originally inspired by the [work here](https://github.com/Gurdhhu/bioinf_scripts) for dealing with nucleotide sequences and more tools will be added as needed. This toolbox requires python 3 and can be installed.

## Table of contents
* [Installation](#installation)
* [biostats cli tools](#biostats-cli-tools)
    * [blasthit](#org-list)


## Installation
This assumes that you have native python 3 & pip installed in your system, you can test this by going to the terminal (or windows command prompt) and trying

```python``` and then ```pip list```

If you get no errors and you have python 3 or higher you should be good to go. To install **biostats** you can install using two methods

```pip install biostats```

or you can also try

```pip install biostats --user```

or you can also try

```
git clone https://github.com/samapriya/biostats.git
cd biostats
python setup.py install
```

Installation is an optional step; the application can be also run directly by executing pydrop.py script. The advantage of having it installed is being able to execute porg as any command line tool. I recommend installation within virtual environment. If you don't want to install, browse into the biostats folder and try ```python biostats.py -h``` to get to the same result.

## biostats cli tools
This is a command line tool and it is designed to simply call the tools you need.

```
usage: biostats.py [-h] {blasthit} ...

Bio tools addons

positional arguments:
  {blasthit}
    blasthit  Annotation of blast results saved in Hit Table CSV format

optional arguments:
  -h, --help  show this help message and exit
```

### blasthit
This script is intended for taxonomic annotation of **blast** results (blastn, tblastn, blastp or blastx) saved in **Hit Table CSV** format where GenBank accession numbers are in the 4th column. It uses **efetch** function from **Bio.Entrez** package to get information about accessions from **GenBank Nucleotide (Nuccore)** or **Protein** databases.
The output is an annotated CSV file "*_annotated.csv" with the following columns added:

* Record name
* Species name
* Full taxonomy
* Reference
* Date of update

![biostats_bhits](https://user-images.githubusercontent.com/6677629/89095362-21e0e580-d39b-11ea-82f8-e2967d898a64.gif)

| arguments | description |
| --- | --- |
| path | Pathway to csv-formatted Hit Table file with blastn results. Positional argument |
| db | For the output of **nucleotide blast** or **tblastn**, use <code>n</code>. For the output of **protein blast** or **blastx**, use <code>p</code>. Positional argument |
| email | Your NCBI email. Positional argument |
| -h, --help | Show help message and exit. Optional argument |
flake8-cognitive-complexity 0.1.0
An extension for flake8 that validates cognitive functions complexity
License: MIT
Requires Python: >=3.6
Keywords: flake8

# flake8-cognitive-complexity

[![Build Status](https://travis-ci.org/Melevir/flake8-cognitive-complexity.svg?branch=master)](https://travis-ci.org/Melevir/flake8-cognitive-complexity)
[![Maintainability](https://api.codeclimate.com/v1/badges/579738d149e489c631a6/maintainability)](https://codeclimate.com/github/Melevir/flake8-cognitive-complexity/maintainability)
[![Test Coverage](https://api.codeclimate.com/v1/badges/579738d149e489c631a6/test_coverage)](https://codeclimate.com/github/Melevir/flake8-cognitive-complexity/test_coverage)
[![PyPI version](https://badge.fury.io/py/flake8-cognitive-complexity.svg)](https://badge.fury.io/py/flake8-cognitive-complexity)
![PyPI - Python Version](https://img.shields.io/pypi/pyversions/flake8-cognitive-complexity)

An extension for flake8 that validates cognitive functions complexity.

Cognitive complexity is analog of cyclomatic complexity, that measure
how difficult to understand piece of code. Introduced by [G. Ann Campbell](https://github.com/ganncamp)
and currently used by SonarSource, CodeClimate and others.
You can find more readings about cognitive complexity in
[cognitive-complexity readme file](https://github.com/Melevir/cognitive_complexity/blob/master/README.md#what-is-cognitive-complexity).

Default complexity is 7, can be configured via `--max-cognitive-complexity` option.

## Installation

```terminal
pip install flake8-cognitive-complexity
```

## Example

```python
def f(a, b):
    if a:
        for i in range(b):
            if b:
                return 1
```

Usage:

```terminal
$ flake8 --max-cognitive-complexity=3 test.py
text.py:1:5: CCR001 Cognitive complexity is too high (6 > 3)
```

Tested on Python 3.7.x and flake8 3.7.8.

## Error codes

| Error code |                     Description          |
|:----------:|:----------------------------------------:|
|   CCR001   | Cognitive complexity is too high (X > Y) |