EthanHolleman

import csv

GENES = set(['PML', 'OAS2', 'OASL', 'IRF7', 'OAS1', 'OAS3', 'BTBD1', 'BTBD2', 'IRF3', 'GBP1'])
# set of target genes
CGI = ''  # G2R file path here
OUT = ''  # output directory here

def find_genes():
    results = {}
    with open(CGI) as C:

EthanHolleman

def subset_sum(l, k):  # l = list values, k is subset sum
    l = sorted(l, reverse=True)
    subset = set([])
    for i in l:
        if k >= i and i not in subset:
            k-= i
            subset.add(i)
        if k == 0:
            break
    return subset

EthanHolleman

lines = []
f_set = set([])

with open('NATIONAL_FACILITY_FILE.CSV') as big:

	for i, row in enumerate(big):
		s = row.split(',')
		if len(s) >= 10:
			if s[6] == '"COOK"' and s[9] == '"ILLINOIS"':
				lines.append(row)

EthanHolleman

lines = []
f_set = set([])

with open('NATIONAL_FACILITY_FILE.CSV') as big:
	for i, row in enumerate(big):
		s = row.split(',')
		if len(s) >= 7:
			if s[6] == '"COOK"':
				lines.append(row)
				f_set.add(s[1])

EthanHolleman

# script to plot the locations and number of LTR predictions for repens
# genome scaffolds. Previously thought that only scaffolds where present but
# some of the entries are labeled as chromosomes. Additionally, LTR elements
# almost exclusively predicted in the chromosome regions. chromosome predictably
# much longer than any single scaffold, not sure if they are seperate / unique
# from all scaffold sequences.

import csv

import matplotlib.pyplot as plt

EthanHolleman

import requests
from bs4 import *
url = 'https://www.cattle-exchange.com/'


req = requests.get(url)
homePage = BeautifulSoup(req.text, 'html.parser')
breeds = (homePage.find("ul", {"class" : "views-summary"})).contents

extensions = []

EthanHolleman

import java.io.*;
import java.util.*;


public class Text {
	private ArrayList<String> words = new ArrayList<String>();
	private ArrayList<String> dictionary;
	
	
	public Text() { //default contructor

EthanHolleman

import os
a,b,c,d = 0,0,0,0

with open("commands.txt", "w") as list:

    command = "bowtie2 -x V1V1Index -r LTRCon.txt -a -S test.sam --non-deterministic -p 4"
    os.system(command)
    print("command executed")
    os.system("samtools view test.sam | wc -l > commandsNums.txt")

EthanHolleman

import openpyxl

wb = openpyxl.load_workbook('Buzz.xlsx')
sheets = wb.sheetnames
names = []
emails = []

for i in sheets: #loops through 4 sheets in the file
    current = wb[i]

EthanHolleman

#This code assumes that scripts are kept in bin file and all other folders are within bin

import os
import random

def makeBlastDB(title, inputFilePath, out): #makes local blast database
    blastCommand = "makeblastdb -dbtype nucl -in {} -title {} -out {}".format(inputFilePath, title, out)
    print(blastCommand)
    os.system(blastCommand)