mparker2

import itertools as it
from functools import partial
from multiprocessing import Pool
import numpy as np
import pandas as pd
import click


EA_TYPES = {
    'contig': str,

mparker2

import re
from argparse import ArgumentParser

parser = ArgumentParser()
parser.add_argument("-g", "--gtf-file", help="Input gtf file",
                    required=True)
parser.add_argument("-o", "--output-prefix", required=True,
                    help="Prefix of the ouput file")

def get_gtf_attribute(gtf_record, attribute):

mparker2

import sys
from collections import Counter
from functools import partial
import numpy as np
import pandas as pd
import pysam
import click


def load_bams(bam_fns):

mparker2

import numpy as np
from scipy.spatial.distance import cdist
from .dtw import dtw
from .lb import envelope, lb_keogh_cdist, lb_keogh_from_bounds
from .window import window_ts

def dtw_nearest_neighbours(query, db, bound_reach, step_size, subseq=False):
    assert query.ndim == 1
    assert db.ndim == 2
    assert query.flags.contiguous

mparker2

import sys
from random import shuffle
from collections import Counter, defaultdict
import pysam
import click
import networkx as nx


def edit_distance(umi_a, umi_b):
    '''

mparker2

import sys
import os
import re
import argparse
import subprocess
from bs4 import BeautifulSoup
from pandas import to_datetime


def check_pattern(job, pattern):