sloria

The Best of the Best Practices (BOBP) Guide for Python

A "Best of the Best Practices" (BOBP) guide to developing in Python.

In General

Values

• "Build tools for others that you want to be built for you." - Kenneth Reitz
• "Simplicity is alway better than functionality." - Pieter Hintjens

willmasters

# 

sudo su -

cd /usr/local/bin
mkdir ffmpeg

cd ffmpeg
wget https://www.johnvansickle.com/ffmpeg/old-releases/ffmpeg-4.2.1-amd64-static.tar.xz
tar xvf ffmpeg-4.2.1-amd64-static.tar.xz

conormm

R to python data wrangling snippets

The dplyr package in R makes data wrangling significantly easier. The beauty of dplyr is that, by design, the options available are limited. Specifically, a set of key verbs form the core of the package. Using these verbs you can solve a wide range of data problems effectively in a shorter timeframe. Whilse transitioning to Python I have greatly missed the ease with which I can think through and solve problems using dplyr in R. The purpose of this document is to demonstrate how to execute the key dplyr verbs when manipulating data using Python (with the pandas package).

dplyr is organised around six key verbs:

fomightez

# List unique values in a DataFrame column
df['Column Name'].unique()

# To extract a specific column (subset the dataframe), you can use [ ] (brackets) or attribute notation.
df.height
df['height']
# are same thing!!! (from http://www.stephaniehicks.com/learnPython/pages/pandas.html 
# -or-
# http://www.datacarpentry.org/python-ecology-lesson/02-index-slice-subset/)

bsweger

Useful Pandas Snippets

A personal diary of DataFrame munging over the years.

Data Types and Conversion

Convert Series datatype to numeric (will error if column has non-numeric values)
(h/t @makmanalp)

jakevdp

willmcgugan

import mmap


def get_last_lines(path: str, count: int) -> list[str]:
    """Get count last lines from a file."""
    with open(path, "r+b") as text_file:
        text_mmap = mmap.mmap(text_file.fileno(), 0, mmap.ACCESS_READ)
        position = len(text_mmap)
        while count and (position := text_mmap.rfind(b"\n", 0, position)) != -1:
            count -= 1

slowkow

#!/usr/bin/env python
"""
GTF.py
Kamil Slowikowski
December 24, 2013

Read GFF/GTF files. Works with gzip compressed files and pandas.

    http://useast.ensembl.org/info/website/upload/gff.html

iamatypeofwalrus

What

Roll your own iPython Notebook server with Amazon Web Services (EC2) using their Free Tier.

What are we using? What do you need?

• An active AWS account. First time sign-ups are eligible for the free tier for a year
• One Micro Tier EC2 Instance
• With AWS we will use the stock Ubuntu Server AMI and customize it.
• Anaconda for Python.
• Coffee/Beer/Time

sminot

import os
from functools import lru_cache
from collections import defaultdict

# Read in the taxonomy
class NCBITaxonomy():
    def __init__(self, folder):
        self.tax = defaultdict(dict)
        # Read in the file of taxid information
        names_fp = os.path.join(folder, 'names.dmp')