vsbuffalo

import numpy as np
from itertools import combinations
from collections import Counter
import datetime as dt

np.random.seed(0)

def repeat_mutation_sim(G, N, L, mu=3e-8):
    """
    Generate N repeats of length L mutating at rate

vsbuffalo

# use GNU screen's C-a binding, since it's programmed in my brain
set-option -g prefix C-a
unbind C-b

# use GNU screen's C-a C-a for last window
bind-key C-a last-window

# use 1-based indexing, since 1 is close
set -g base-index 1

vsbuffalo

#!/bin/bash
# trim.sh - generic, slightly insane paired end quality trimming script
# Vince Buffalo <vsbuffaloAAAAAA@gmail.com> (sans poly-A)
set -e
set -u

## pre-config
ADAPTERS=illumina_adapters.fa
SAMPLE_NAME=some_sample_name
IN1=in1.fastq

vsbuffalo

"""

Generate a IUPAC nucleotide table. The order is a modification of Heng
Li's. I have added '-' to mean gap. X means non-IUPAC character and
can be a useful warning.

"""
import sys
rev_iupac = "XACMGRSVTWYHKDBN-"
rev_iupac_alt = "xacmgrsvtwyhkdbn."

vsbuffalo

tail -f your_mapping.sam |  bioawk -csam 'BEGIN{total=0;mapped=0} {total = total + 1; mapped = mapped + !and($flag, 4); if (total % 100 == 0) { printf "\tmapping rate: %f\r",mapped/total }}'

vsbuffalo

trashpanda <- function() {
  if (!require('ecoengine')) {
    install.packages("ecoengine", dependencies = TRUE)
    library(ecoengine)
  }
  view_photos(ee_photos(scientific_name = "Procyon lotor", quiet = TRUE))
}

vsbuffalo

/* 
(c) Vince Buffalo, 2012; License: GPL.
I compile this on my system (OS X with samtools installed via Homebrew) with:

    clang -g -lz -L/usr/local/Cellar/samtools/0.1.18/lib/ -lbam -I/usr/local/Cellar/samtools/0.1.18/include/bam/ -o mapqcov mapqcov.c

But you'll likely need to compile differently for you libraries. This code works and is consistent with the slower results from mpileup. This is just a standalone beta; it will likely be incorporated into something else.
*/

#include <stdio.h>

vsbuffalo

# hmmerfix.py - fix terrible output format (fixed width) of HMMER

# We make a simple assumption about the data: any non-delimiter spaces
# are in the last column. Under this assumption, we build a regular
# expression programmatically with strict types. Strict typing and the
# number of grouped elements ensure some safety.

import re
import sys
from collections import OrderedDict

vsbuffalo

The Ten Commandments of Scientific Coding

1. Thou shall use version control.

2. Thou shall comment thy code.

3. Thou shall use existing libraries whenever possible.

4. Thou shall try to unit test.

vsbuffalo

For every minute you are angry, you lose sixty seconds of happiness. ::: unknown
Anger is a momentary madness, so control your passion or it will control you. ::: Horace Walpole
When angry, count ten before you speak; if very angry, a hundred. ::: Jefferson
Anger is a wind which blows out the lamp of the mind. ::: Robert G. Ingersoll
Holding on to anger is like grasping a hot coal with the intent of throwing it at someone else; you are the one getting burned. ::: Buddha
The best remedy for a short temper is a long walk. ::: Jacqueline Schiff