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import random | |
import argparse | |
parser = argparse.ArgumentParser( description="https://www.youtube.com/watch?v=7S94ohyErSw&t=90") | |
parser.add_argument("-t", "--tests", default=50, type=int, help='The number of tests to average') | |
parser.add_argument("-tp", "--true_positives", required=True, type=int, help='The actual number of True Positives') | |
parser.add_argument("-tn", "--true_negatives", required=True, type=int, help='The actual number of True Negatives (Total things - True Positives)') | |
parser.add_argument("-tpa", "--true_positives_A", required=True, type=int, help='True Positives tool A detects') | |
parser.add_argument("-fpa", "--false_positives_A", required=True, type=int, help='False Positives tool A detects') | |
parser.add_argument("-tpb", "--true_positives_B", required=True, type=int, help='True Positives tool B detects') |
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if [ "`tail -c 28 /path/to/your.bam`" != "`echo -n -e '\x1f\x8b\x08\x04\x00\x00\x00\x00\x00\xff\x06\x00\x42\x43\x02\x00\x1b\x00\x03\x00\x00\x00\x00\x00\x00\x00\x00\x00'`" ]; then echo 'File Truncated'; else echo 'File Good!'; fi |
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#!/usr/bin/env python3 | |
import os | |
import csv | |
import argparse | |
parser = argparse.ArgumentParser(description='Process output from Mash') | |
parser.add_argument('-i', '--input', help='input file', metavar='FILE', required=True) | |
parser.add_argument('-o', '--output', help='output file', metavar='FILE' ) | |
parser.add_argument('-a', '--alias', help='alias file', metavar='FILE' ) | |
parser.add_argument('-n', '--nearness', help='invert distance',action="store_true" ) |
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class stat: | |
def __init__(self,INFO): | |
self.DESCRIPTION = ['Demo for harmbrugge', 'ENSMUSG00000051951'] | |
self.LINKABLE = True | |
self.SQL = 'TEXT' | |
self.dependencies = ['CHR','POS','SEQ'] | |
self.before = ''' | |
import intervaltree | |
GTF_chromosomes = {} | |
with open('/Users/John/Downloads/Mus_musculus.GRCm38.86.gtf','rb') as f: |
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import sys | |
reads = sys.argv[1] | |
index = sys.argv[2] | |
all_readIDs = set() | |
# Re-written the code below to only ever read the first row: | |
with open(reads, "r") as read_file: | |
while True: | |
try: | |
line1 = next(read_file) |
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import sys | |
reads = sys.argv[1] | |
index = sys.argv[2] | |
# Get all read ids: | |
all_readIDs = set() # Using a set because it will be quicker to find things in later. | |
# A list would require python to check every item in the list. | |
# A set can be thought of as an always-sorted list (elements are added in their sorted order) with no duplication of elements. | |
# The sorted order is based on the hash() value of the items however, which is essentially a random number. |
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# Stuff you might have to change depending on your package manager the IP of your client: | |
# (these settings will work well for EC2 though) | |
Listen 10.8.0.1 | |
User tinyproxy | |
Group tinyproxy | |
# More is better/faster: | |
MinSpareServers 10 | |
MaxSpareServers 50 | |
StartServers 25 |
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# Non-Windows only: | |
user nobody | |
group nogroup | |
# Common for everything else: | |
client | |
dev tun | |
proto tcp-client | |
remote 54.152.94.74 443 | |
resolv-retry infinite |
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# STUFF YOU COULD CHANGE TO REFLECT YOUR SYSTEM BETTER: | |
export KEY_COUNTRY="UK" | |
export KEY_PROVINCE="London" | |
export KEY_CITY="London" | |
export KEY_ORG="MyVPN" | |
export KEY_EMAIL="[email protected]" | |
export KEY_OU="MyVPN" | |
# STUFF YOU SHOULDNT CHANGE | |
export EASY_RSA="/etc/openvpn/easy-rsa" |
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management localhost 6666 # Allows you to telnet into localhost 6666 to see the status. Although openvpn has logs, you can find out a lot more (like who is currently using on the VPN) through the management service | |
port 443 # By using port 443 for all of our VPN communications, our network traffic will look very similar to standard HTTPS traffic. | |
client-to-client # Allows two clients of the VPN to talk to one another (home computer to work computer for example) | |
keepalive 10 120 # Defaults | |
mssfix # Kept due to Cargo Cult reasons... | |
proto tcp # udp is faster, but so much less reliable its not worth it. Use TCP. | |
dev tun # We're making a tunnel so we want to make the tun kind of VPN. | |
ca ca.crt # we'll make this next | |
cert server.crt # we'll make this next | |
key server.key # we'll make this next |
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