turtlemonvh

Sequence alignment

While watching some videos from Udacity describing sequence alignment I was having a bit of a hard time understanding the algorithm as it was explained, so I decided to write it in code.

This is a fairly simple approach and uses recursion (so stack depth may be a problem for larger sequences), but it does use dynamic programming to keep things relatively fast. The code uses the same N, NW, W notation the video uses to describe the problem graph.

If there are branches in the problem graph (i.e. 2 alignments are have the same score) the program just takes the first solution.

Sequence alignment video series (part of the "Computability Complexity and Algorithms" class on Udacity): https://www.youtube.com/watch?v=3NLYH44F6SU&index=5&list=PLAwxTw4SYaPkbWSEj_1iO7rILlWDJImW4

turtlemonvh

A function to get the values of all non-private properties of an object

showprops = lambda p: [(prop, getattr(p, prop)) for prop in [lprop for lprop in dir(p) if not lprop.startswith("_")]]

Example usage from an ipython shell

# Parse a complicated uri
In [1]: from urlparse import urlparse
In [2]: uri = "postgresql+psycopg2://user:password@postgres:5432/default"

In [3]: p = urlparse(uri)

turtlemonvh

Go Get from Stash

Add this function to your ~/.bashrc.

Use like

# Just use the url that stash recommends for cloning over ssh
go-get-stash ssh://git@stash.in.ionicsecurity.com:7999/il/common.git

You can use this package in your go files like

turtlemonvh

Go retime objectid experiment

The mgo library has a function for generating an id with a timestamp (https://godoc.org/labix.org/v2/mgo/bson#NewObjectIdWithTime), but all the non-time related fields are zeroed out. This is useful for time range comparisons, but kind of annoying if you want to generate a new ObjectId for a particular time range that may be in the past or future.

This example shows how to take an existing unique ObjectId and adjust its origin time.

Example output

turtlemonvh

Pocket bookmarklet

This version of the pocket bookmarklet seems to work fine pretty much everywhere, but has issues on this page: https://queue.acm.org/detail.cfm?id=2745840

turtlemonvh

#!/usr/bin/env bash

# Ensure ruby tools needed for FPM are available
apt-get install -y ruby ruby-dev gem rpm

# Ensure FPM is installed 
gem install fpm

# Run FPM to build an image
fpm -s python \

turtlemonvh

Mezzanine template tag for longer post description

If you want more options than just showing a single line of text in your blog post listings, this may be useful.

First, make sure you have copied the mezzanine base templates into your application where you can edit them.

See this part of the docs if you missed that step: http://mezzanine.jupo.org/docs/frequently-asked-questions.html#where-are-all-the-templates-i-can-modify

Use

turtlemonvh

Find structural diffs

A simple script to show the structural differences between json files.

Usage

# Pairwise diffs between all files ending with `.json` in the current directory
python record-template-diffs.py

Pairswise diffs between every file ending in allowed.json in the current directory

turtlemonvh

# If the file you need to source is `.setup-env`
[e.split("=")[0:2] for e in commands.getoutput(". .setup-env && env").split("\n")]

turtlemonvh

# Print byte counts in a human-friendly way

def human_bytes(b):
    kb = 1024
    mb = kb*1024
    gb = mb*1024
    tb = gb*1024

    if b < 1024:
        return "%d b" % b