dnanto

#!/usr/bin/env bash

# ideally, set this outside of this script, like in a profile
export BEAST_PACKAGE_PATH="$(pwd)"/.pkg

arr=(
	"https://github.com/BEAST2-Dev/BEASTLabs/releases/download/v1.9.0/BEASTlabs.addon.v1.9.2.zip"
	"https://github.com/BEAST2-Dev/bModelTest/releases/download/v1.2.0/bModelTest.addon.v1.2.1.zip"
	"https://github.com/BEAST2-Dev/model-selection/releases/download/v1.5.0/MODEL_SELECTION.addon.v1.5.2.zip"
	"https://github.com/BEAST2-Dev/nested-sampling/releases/download/v1.1.0/NS.addon.v1.1.0.zip"

dnanto

library(tidyverse)
library(igraph)

parse_attr <- function(val)
{
  tokens <- 
    str_split(val, '(,)(?=(?:[^"]|"[^"]*")*$)') %>%
    lapply(str_split, '(=)(?=(?:[^"]|"[^"]*")*$)') %>%
    unlist() %>% 
    str_trim() %>%

dnanto

def parse_coor(coor):
    return int(coor[0].lstrip(">").lstrip("<")), int(coor[1].lstrip(">").lstrip("<"))

def parse_ft(file):
    acc, feat, coors, anno = None, None, None, None
    for line in map(str.rstrip, file):
        if line.startswith(">Feature"):
            acc = line[9:].split("|", maxsplit=2)[1].split(".")[0]
        elif acc and line:
            if not line[0].isspace():

dnanto

library(tidyverse)

geomid <- function(lat, lon)
{
  # http://www.geomidpoint.com/calculation.html
  lat <- lat * pi / 180
  lon <- lon * pi / 180
  x <- mean(sum(cos(lat) * cos(lon)))
  y <- mean(sum(cos(lat) * sin(lon)))
  z <- mean(sum(sin(lat)))

dnanto

read_ft <- function(file) {
  # read tsv with a maximum of five columns
  suppressWarnings(
    read_tsv(
      file,
      col_names = c("start", "end", "name", "key", "val"),
      col_types = cols(.default = "c")
    )
  ) %>%
    # associate rows with a feature accession and feature identifier number

dnanto

#!/usr/bin/env python3

__author__ = "dnanto"

import json
import sys
from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser, FileType
from pathlib import Path

from Bio.PDB import PDBParser, Superimposer