trvinh

from ete3 import NCBITaxa
ncbi = NCBITaxa()
ncbi.update_taxonomy_database()

trvinh

library(PhyloProfile)

processNcbiTaxonomy <- function(taxdmpfile = NULL) {
    if (is.null(taxdmpfile) || !file.exists(taxdmpfile)) {
        stop("taxdmp.zip file invalid!")
    } else temp <- taxdmpfile
    
    names <- utils::read.table(
        unz(temp, "names.dmp"), header = FALSE, fill = TRUE, sep = "\t",
        quote = "", comment.char = "", stringsAsFactors = FALSE

trvinh

# -*- coding: utf-8 -*-

from Bio import SeqIO
import argparse
import shutil

def combine_fa(fa_1, fa_2, out_file):
    """ Combine 2 fasta files """
    new_fa_dict = SeqIO.to_dict(SeqIO.parse(open(fa_2),'fasta'))
    existing_seq = SeqIO.to_dict(SeqIO.parse(open(fa_1),'fasta'))

trvinh

library(PhyloProfile)

setwd('PhyloProfile/data')

# load data 
data(taxonNamesReduced)
# modify the dataframe
# for example, rename Actinobacteria to Actinomycetota
taxonNamesReduced$fullName[
    taxonNamesReduced$rank == "phylum" & taxonNamesReduced$ncbiID == 201174

trvinh

import timeit

def test(st,en): 
    return random.randint(st, en)

t = timeit.Timer(lambda: test(10, 100))
print(t.timeit(10))

trvinh

#!/bin/env python

############################################
#                                          #
# Update domain files with intepro IDs     #
#                                          #
############################################

import sys
import os

trvinh

#!/bin/env python

import sys
import os
from pathlib import Path
import re
import json
import shutil
import subprocess
import argparse

trvinh

library(PhyloProfile)
library(data.table)
library(tidyr)

args = commandArgs(trailingOnly=TRUE)
idListFile <- args[1]
idListDf <- read.csv(idListFile, stringsAsFactors = FALSE, header = FALSE)
type <- args[2]

firstup <- function(x) {

trvinh

library(PhyloProfile)
library(data.table)
library(tidyr)

args = commandArgs(trailingOnly=TRUE)
idListFile <- args[1]
idListDf <- read.csv(idListFile, stringsAsFactors = FALSE, header = FALSE) # data.table::fread(idListFile)

type <- args[2]

trvinh

Source: 01 02

# install xcode (if not yet)
xcode-select --install

# install homebrew (if not yet)
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

### STEP 1: install ruby and jekyll