Daniel Antonio Negrón dnanto

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dnanto / rmsd.py

Created March 8, 2024 17:07

Calculate RMSD using Biopython

	#!/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 / ft.R

Created May 5, 2021 16:42

R function to read the NCBI BankIT Feature Table file format using the tidyverse package

	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 / geomid.R

Created June 25, 2020 18:14

Calculate the geographic midpoint given a list of geographic coordinates in R.

	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 / ft.py

Created May 4, 2020 14:46

Parse the Feature Table format of Entrez Direct E-utilities.

	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 / dot.R

Last active April 8, 2020 16:25

R function to read a DOT file into an igraph obj

dnanto / pkg.sh

Created March 18, 2020 17:27

Manual installation of BEAST2 v2.5.0+ packages...

	#!/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 / snp-sites-counts.R

Last active March 9, 2020 17:55

snp-sites VCF to SNP counts...

	# 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 / lsystem.py

Created January 10, 2020 05:41

L-system string generator in python...

	#!/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 / rbtop.R

Created December 31, 2019 22:07

calculate the reverse complement of a BTOP string (uses tidyverse)

	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 / btop.R

Created September 21, 2019 16:35

decode mutations from BTOP string in R (uses tidyverse)

	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))
	}