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@bhtucker
bhtucker / upsert.py
Last active February 17, 2025 15:08
A demonstration of Postgres upserts in SQLAlchemy
"""
Upsert gist
Requires at least postgres 9.5 and sqlalchemy 1.1
Initial state:
[]
Initial upsert:
@mikelove
mikelove / accession2url.R
Created June 16, 2016 18:33
ENA accession to URL
accession2url <- function(x) {
prefix <- "ftp://ftp.sra.ebi.ac.uk/vol1/fastq"
dir1 <- paste0("/",substr(x,1,6))
dir2 <- ifelse(nchar(x) == 9, "",
ifelse(nchar(x) == 10, paste0("/00",substr(x,10,10)),
ifelse(nchar(x) == 11, paste0("/0",substr(x,10,11)),
paste0("/",substr(x,10,12)))))
paste0(prefix,dir1,dir2,"/",x)
}
# -*- coding: utf-8 -*-
"""Example Google style docstrings.
This module demonstrates documentation as specified by the `Google Python
Style Guide`_. Docstrings may extend over multiple lines. Sections are created
with a section header and a colon followed by a block of indented text.
Example:
Examples can be given using either the ``Example`` or ``Examples``
sections. Sections support any reStructuredText formatting, including
@veselosky
veselosky / s3gzip.py
Last active August 29, 2024 11:32
How to store and retrieve gzip-compressed objects in AWS S3
# vim: set fileencoding=utf-8 :
#
# How to store and retrieve gzip-compressed objects in AWS S3
###########################################################################
#
# Copyright 2015 Vince Veselosky and contributors
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
@quiver
quiver / retrieve-EC2-region-information-from-metadata.md
Last active March 14, 2024 16:42
retrieve EC2's region from instance metadata

Sometimes you want to retrieve EC2 insntances' region information.

You can query that information through instance metadata(169.254.169.254).

$ curl --silent http://169.254.169.254/latest/dynamic/instance-identity/document
{
  "privateIp" : "172.31.2.15",
  "instanceId" : "i-12341ee8",
  "billingProducts" : null,
 "instanceType" : "t2.small",
@jtpaasch
jtpaasch / amazonctl.py
Created October 26, 2015 12:47
A collection of functions commonly used to do AWS stuff.
# -*- coding: utf-8 -*-
"""A simple tool to document how to control AWS resources.
AWS AUTHENTICATION
-------------------
In order to run any of the code below, you need a profile with AWS credentials
set up on your computer. It's very easy to do this. Google how to configure
your profile with boto3, or visit the docs:
@jennybc
jennybc / 2014-10-12_stop-working-directory-insanity.md
Last active February 19, 2025 22:20
Stop the working directory insanity

There are packages for this now!

2017-08-03: Since I wrote this in 2014, the universe, specifically Kirill Müller (https://github.com/krlmlr), has provided better solutions to this problem. I now recommend that you use one of these two packages:

  • rprojroot: This is the main package with functions to help you express paths in a way that will "just work" when developing interactively in an RStudio Project and when you render your file.
  • here: A lightweight wrapper around rprojroot that anticipates the most likely scenario: you want to write paths relative to the top-level directory, defined as an RStudio project or Git repo. TRY THIS FIRST.

I love these packages so much I wrote an ode to here.

I use these packages now instead of what I describe below. I'll leave this gist up for historical interest. 😆

@LeCoupa
LeCoupa / bash-cheatsheet.sh
Last active April 2, 2025 18:42
Bash CheatSheet for UNIX Systems --> UPDATED VERSION --> https://github.com/LeCoupa/awesome-cheatsheets
#!/bin/bash
#####################################################
# Name: Bash CheatSheet for Mac OSX
#
# A little overlook of the Bash basics
#
# Usage:
#
# Author: J. Le Coupanec
# Date: 2014/11/04
@rmflight
rmflight / post-commit
Last active March 29, 2024 19:43
useful commit hooks for R package dev
#!/path/2/Rscript
# License: CC0 (just be nice and point others to where you got this)
# Author: Robert M Flight <[email protected]>, github.com/rmflight
#
# This is a post-commit hook that after a successful commit subsequently increments the package version in DESCRIPTION
# and commits that. Analogous to the pre-commit at https://gist.github.com/rmflight/8863882, but useful if you only have
# good reasons for not doing it on the pre-commit.
#
# To install it, simply copy this into the ".git/hooks/post-commit" file of your git repo, change /path/2/Rscript, and make
@sloria
sloria / bobp-python.md
Last active March 3, 2025 16:09
A "Best of the Best Practices" (BOBP) guide to developing in Python.

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