guillermo-carrasco

diff -ru simNGS.orig/src/simlibrary.c simNGS/src/simlibrary.c
--- simNGS.orig/src/simlibrary.c  2013-05-13 17:45:17.000000000 +0200
+++ simNGS/src/simlibrary.c	2013-05-13 18:06:41.000000000 +0200
@@ -33,12 +33,13 @@
 #define QUOTE(A) Q_(A)
 #define DEFAULT_COV         0.055
 #define DEFAULT_OUT         "fasta"
+#define DEFAULT_UNIQUE      "not"
 #define DEFAULT_INSERT      400
 #define DEFAULT_NCYCLE      45

guillermo-carrasco

/*
Deinterleave FASQ files containing both reads from a paired-end read.
The script makes the following assumption:
    * FASTQ format (4 lines per read), and the two reads (fordward and reverse) in a row.

USAGE: :/deinterleave file.fastq  f.file.fastq r.file.fastq
RESULT: f.file.fastq r.file.fastq containing fordward and backward reads, respectively

Can deinterleave FASTQ files of any size, does not consume memory. The execution time is
I/O bounded.

guillermo-carrasco

import logging
from logbook.queues import RedisHandler

h = RedisHandler(key='python_agent')
l = logging.getLogger('redis')
l.addHandler(h)

l.warn('hejjjjjj')

guillermo-carrasco

In this step we'll create a swarm cluster from two nodes. You should've received access to two nodes in AWS.

1. SSH in to the first node: ssh -i docker_demo.pem ubuntu@IP1
2. Figure out the internal IP address of the node: ifconfig and check the eth0 address (10.0....)
3. Initialize the Swarm cluster: `docker swarm init --listen-addr INTERNAL_IP --advertise-addr INTERNAL_IP
4. Open a new tab and SSH to the other node: ssh -i docker_demo.pem ubuntu@IP2
5. Check the internal IP of that node: ifconfig and eth0
6. Join to the cluster with the command the previous command printed out. Before executing the command, you need to the extend it with the --listen-addr and --advertise-addr parameters (using the internal IP of the second node): docker swarm join TOKEN --listen-addr 10.0.... --advertise-addr 10.0..... node1...
7. Get back to the first node and verify the results: docker node ls

guillermo-carrasco

version: 1
formatters:
    custom_format:
        format: "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
filters:
    myapp:
        name: myapp
handlers:
    console:
        class: logging.StreamHandler

guillermo-carrasco

import logging

parent_log = logging.getLogger('parent')
child_1 = logging.getLogger('parent.child_1')
child_2 = logging.getLogger('parent.child_2')

guillermo-carrasco

import yaml
import logging
import logging.config

with open('config.yaml', 'r') as f:
    conf = yaml.load(f)

logging.config.dictConfig(conf)

myapp = logging.getLogger('myapp')

guillermo-carrasco

import glob
import os
import random

if not os.path.exists('selected.txt'):
    open('selected.txt', 'a').close()

with open('selected.txt', 'r') as f:
    selected = f.read().splitlines()

guillermo-carrasco

import argparse
import logging
import re
import subprocess
import sys
from pathlib import Path
from typing import List


def fetch_latest_version(library):

guillermo-carrasco

import re
from collections import Counter
from datetime import datetime

import emoji
import pandas as pd

class WhatsappChat:
    DATE_FORMAT = "[%m/%d/%y, %H:%M:%S]"