EthanHolleman

[[ $- = *i* ]] && source ~/bin/liquidprompt/liquidprompt

export LS_COLORS='rs=0:di=01;34:ln=01;36:mh=00:pi=40;33'
alias ls='ls --color=always'
export PATH="/home/ethollem/software/bpipe-0.9.10/bin:$PATH"
export PATH="~/bin:$PATH"

EthanHolleman

CACGTCCTAAAAGTGACCAG
CACCCCCTGCTCCTGGCGCT
GGGTGGGCACGCTCCTCCCT
ATCACGCCCGGAGGAGGGCG
CTGGCCGCCCCCAGCCACCC
GGTCCCTGCAGAAGCGTGGC
GGAGGACGTGGCTGGGCTCG
GCAACTAGACGCAGCCCGCA
AGCCGCAGCCTTTGTGAACC
GAATAAAGCCCTTGAACCAG

EthanHolleman

>NG_007114.1:4986-6416 Homo sapiens insulin (INS), RefSeqGene on chromosome 11
AGCCCTCCAGGACAGGCTGCATCAGAAGAGGCCATCAAGCAGGTCTGTTCCAAGGGCCTTTGCGTCAGGT
GGGCTCAGGATTCCAGGGTGGCTGGACCCCAGGCCCCAGCTCTGCAGCAGGGAGGACGTGGCTGGGCTCG
TGAAGCATGTGGGGGTGAGCCCAGGGGCCCCAAGGCAGGGCACCTGGCCTTCAGCCTGCCTCAGCCCTGC
CTGTCTCCCAGATCACTGTCCTTCTGCCATGGCCCTGTGGATGCGCCTCCTGCCCCTGCTGGCGCTGCTG
GCCCTCTGGGGACCTGACCCAGCCGCAGCCTTTGTGAACCAACACCTGTGCGGCTCACACCTGGTGGAAG
CTCTCTACCTAGTGTGCGGGGAACGAGGCTTCTTCTACACACCCAAGACCCGCCGGGAGGCAGAGGACCT
GCAGGGTGAGCCAACTGCCCATTGCTGCCCCTGGCCGCCCCCAGCCACCCCCTGCTCCTGGCGCTCCCAC
CCAGCATGGGCAGAAGGGGGCAGGAGGCTGCCACCCAGCAGGGGGTCAGGTGCACTTTTTTAAAAAGAAG
TTCTCTTGGTCACGTCCTAAAAGTGACCAGCTCCCTGTGGCCCAGTCAGAATCTCAGCCTGAGGACGGTG

EthanHolleman

import random
from argparse import ArgumentParser
from itertools import cycle

# Lol you actually clicked the link to read the figure assignment script, NERD!

LAB = ['Aidan',  'Ethan', 'Meghan', 'Stella', 'Talysa', 'Saloni', 'Tadas', 'Deana']
random.shuffle(LAB)

EthanHolleman

#!/bin/bash
# Script for quickly setting up a new snakemake workflow

mkdir workflow
mkdir notes
mkdir resources

# Download license file
wget https://raw.githubusercontent.com/Illumina/licenses/master/gpl-3.0.txt
mv gpl-3.0.txt LICENSE

EthanHolleman

#!/usr/bin/env python3
from pathlib import Path
from Bio import SeqIO
from Bio.Seq import Seq
from argparse import ArgumentParser

FORMAT_DICT = {
    ".fa": "fasta",
    ".fasta": "fasta",
    ".gb": "genbank",

EthanHolleman

#!/usr/bin/env python3

from Bio import SeqIO
from argparse import ArgumentParser
import itertools

def get_args():
    parser = ArgumentParser()
    parser.add_argument('genbank', nargs='+', default=[], help='List of genbank formated files.')
    parser.add_argument('fasta', help='Output path to write fasta records to.')

EthanHolleman

# a target rule to define the desired final output
rule all:
    input:
        "aggregated/a.txt",
        "aggregated/b.txt"


# the checkpoint that shall trigger re-evaluation of the DAG
checkpoint somestep:
    input:

EthanHolleman

import sys
import subprocess
import os
import csv
from datetime import datetime
import re
import json
from pathlib import Path

IP_ADDRESS = '0.0.0.0'

EthanHolleman

HOME = (10, 12)

STOPS = {'Howard_Western': (0,0}, 'Howard_Ridge': (0,3), 'Howard_L': (0,9),
         'Jarvis_Clark' : (2, 8), 'Jarvis_L': (2, 11), 'Touhy_Clark': (4,8),
         'Touhy_Glenwood': (4, 13)}
# additional stops need to be added

BUSES = [((0,0), (11, 0)), ((0, 15), (11, 15)), ((0, 8), (11, 8)),
         ((7, 0), (7, 15)), ((10, 0), (10, 15))]