apcamargo

bootstraps_mann_whitney <- function(bootstraps_number, sample_1, sample_2) {
  differences <- numeric()
  for (i in sample_1) {
    for (j in sample_2) {
      differences[1 + length(differences)] <- i - j
    }
  }
  bootstraps_statistic <- numeric(bootstraps_number)
  hodges_lehmann_estimator <- median(differences)
  sample_1_delta <- sample_1 - hodges_lehmann_estimator

apcamargo

#!/usr/bin/env python
# Changes: python3, argparse, gff3
# check if python >= 3.6

import argparse
import sys


def main(input_file, output_file):
    """Converts a file from the BED (Browser Extensible Data) format to the GFF3 (General Feature Format version 3) format."""

apcamargo

# Requires jupytext (https://github.com/mwouts/jupytext) and Glow (https://github.com/charmbracelet/glow)

ipynb-view () {
    if [ -z "$1" ]; then
        echo "Usage: ipynb-view <notebook.ipynb>";
        return 1;
    fi;
    jupytext --from ipynb --to markdown --output - "$1" | glow --preserve-new-lines --pager
}

apcamargo

import bz2
import gzip
import lzma
from contextlib import contextmanager
from enum import Enum, auto
from pathlib import Path
from typing import TextIO


class Compression(Enum):

apcamargo

import bz2
import gzip
import lzma
import textwrap
from contextlib import contextmanager
from enum import Enum, auto
from pathlib import Path


class Compression(Enum):

apcamargo

#!/usr/bin/env python

# hhblits -v 0 -cpu 1 -n 1 -p 90 -z 0 -Z 5000 -b 0 -B 5000 -M 50 -d busco_db/busco -i msa.faa -o msa.hhr

from collections import namedtuple
from pathlib import Path
import argparse

parser = argparse.ArgumentParser(description='Parse hhsearch hhr output file.')
parser.add_argument('-i', help='input hrr path', dest='input_file',type=str, required=True)

apcamargo

import subprocess

def get_assembly_accession(genbank_accession):
    p1 = subprocess.Popen(
        ["elink", "-db", "nuccore", "-target", "assembly", "-id", genbank_accession],
        stdout=subprocess.PIPE,
        stderr=subprocess.PIPE,
    )
    p2 = subprocess.Popen(
        ["efetch", "-format", "docsum"],

apcamargo

from coloraide import Color


def lighten(
    color: Color,
    amount: float,
) -> Color:
    """
    Lighten a color by a given amount.
    """

apcamargo

apcamargo

#!/usr/bin/env python

import math
import re

import click
from scipy.cluster.hierarchy import fcluster, linkage
from skbio import DistanceMatrix, Protein, TabularMSA, io
from skbio.sequence.distance import hamming