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

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

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

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)
library(igraph)

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

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

# mafft ncov.fna > msa.fna
# snp-sites -c -v msa.fna > snp.vcf
library(tidyverse)
lines <- read_lines("snp.vcf")
fields <- str_split(last(lines[startsWith(lines, "#")]), "\t")[[1]]
read_tsv(lines, comment = "#", col_names = fields, col_types = cols(.default = "c")) %>%
  select(10:ncol(.)) %>%
  mutate_all(as.integer) %>% 
  colSums() %>% 
  sort(decreasing = T) %>% 

dnanto

#!/usr/bin/env python3

import sys

axiom = "0"
rules = { "0": "1[0]0", "1": "11" }

for i in range(int(sys.argv[1])):
    axiom = "".join(rules.get(e, e) for e in axiom)
    print(axiom)

dnanto

comp <- set_names(
  as.list(str_split("TAACGRYSWMKVHDBN", "", simplify = 1)), 
  str_split("ATUGCYRSWKMBDHVN", "", simplify = T)
)

revcomp_btop <- function(btop)
{
  str_replace_all(btop, "([A-Z-])([A-Z-])", " \\2 \\1 ") %>% 
    str_split(" ", simplify = T) %>% 
    rev() %>% 

dnanto

decode_btop <- function(btop)
{
	matches <- as.integer(str_extract_all(btop, "\\d+", simplify = T))
	matches <- if (str_starts(btop, "\\d", negate = T)) c(0, matches) else matches
	pos <- 0; n <- 0; m <- 0; muts <- list();
	for (ele in Filter(nchar, str_split(btop, "\\d+", simplify = T)))
	{
		pos <- pos + matches[n<-n+1]
		for (i in seq(1, nchar(ele), 2)) muts[[m<-m+1]] <- list(pos = pos<-pos+1, mut = substr(ele, i, i+1))
	}