asalt

class Thing:
    def speak(self) -> str:
        raise NotImplementedError("Things don't inherently speak.")

class Rock(Thing):
    def speak(self, msg):
        return ValueError("Rocks cannot speak")

class Plant(Thing):
    def speak(self) -> str:

asalt

from pyteomics import parser, mass
import matplotlib.pyplot as plt

# ============================
# 1. Define protein sequence
# ============================
protein_seq = "RELEELNVPGEIVESLSSSEESITRINKKIEKFQSEEQQQTEDELQDKIHPFAQTQSLVYPFPGPI"

# ============================
# 2. In-silico trypsin digestion

asalt

import numpy as np
import matplotlib.pyplot as plt
import argparse
import os

def generate_vectors(num_slots, num_values, spacing, variance, diff_variance, diff_positions, diff_weight=1, aligned=True):
    """Generate two vectors with specified characteristics."""
    if spacing == "even":
        positions = np.linspace(0, num_slots - 1, num_values, dtype=int)
    else:

asalt

# Load required libraries
library(cmapR)       # For handling GCT files
library(ComplexHeatmap)  # For visualization, see https://jokergoo.github.io/ComplexHeatmap-reference/book/ for a complete reference
library(RColorBrewer) # For color palettes
library(dplyr)

make_random_gct <- function(nrow = 100, ncol = 10) {
  set.seed(369)
  nrow <- max(nrow, 1)
  ncol <- max(ncol, 1)

asalt

import pickle
import hashlib
import time
import os
import pandas as pd
from datetime import datetime

class BaseCache:
    """Base class for caching strategies."""
    def __init__(self):

asalt

"""
Simple script to separate MaxQuant experiments
"""
import os
import sys
import numpy as np
import pandas as pd

def main(f):
    df = pd.read_table(f)

asalt

from functools import wraps

def make_iterable(argn=0, exceptions=[]):
    """Check to make sure an argument is an iterator.
    Default argument is args[0]
    Add exceptions that you wish to enclose in an iterator by providing an
    iterator of their type.
    Ironically, exceptions must be encapsulated in an iterator"""
    def decorate(func):
        @wraps(func)

asalt

%http://tex.stackexchange.com/questions/77920/comment-package-excludecomment-gives-error
\documentclass[12pt]{article}
\usepackage{todonotes} % \missingfigure 
\usepackage{comment} % to exclude whole sections when I want to

\newif\ifshow % toggle true or false based on if want to hide section
%\showtrue % show the sections
\showfalse % hide the sections

\ifshow

asalt

asalt

#check if files in directory aren't in log of previously encountered log
from time import sleep

def filechecker():
    print '{} : Checking for new files...'.format(time.ctime())
    try : log = open('filelog.log','r+U') #open log file in append mode
    except : log = open('filelog.log','ab+') # if it doesn't exist, create it
    files = [line.strip('\n') for line in log.readlines()] # list of all files in log

    for f in os.listdir(inputdir): # iterate through all files in directory