| #!/usr/bin/env python3 | |
| # Author: thanh le viet 12-2019 | |
| import pathlib | |
| import click | |
| import re | |
| @click.command() | |
| @click.option('--pid', default='', help='Project ID') |
| #Install MinKNOW | |
| sudo apt-get update | |
| sudo apt-get install wget | |
| wget -O- https://mirror.oxfordnanoportal.com/apt/ont-repo.pub | sudo apt-key add - | |
| echo "deb http://mirror.oxfordnanoportal.com/apt bionic-stable non-free" | sudo tee /etc/apt/sources.list.d/nanoporetech.sources.list | |
| sudo apt-get update | |
| sudo apt-get install minion-nc | |
| #Install Guppy |
| ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDShCb7OtE+KTv4JWrKzLYZ1Nyul4eppxIRYUCxGdEIGe4Q68m+LR1ZofnojgIrMKV5VGeWv1OUAteHkBC396AMB/bDK7bvHDeN43egiameTlvRXbW7qpnpL+6XkLMOokP9wmMqFE2TVnQstG56LpZfKgVlYQpk9oksxqyUr3jMvA5VSdz191jtEv2KhdZUYELo7thZ6nPTtqYmk2JGuOumekm5l+tRENop6Al3ez09oGAnzJmh9v09o9BPkRXDIwyMN9D1q/Na7SUpe1RrfT1dQY9+YVp7XhPPI+GIcNzMif91xgqt0sMXU+65e3HPjz+feaeWAr966tV+0j5Na1br thanhlv@LVBH |
| library(readxl) | |
| library(readr) | |
| library(dplyr) | |
| library(stringr) | |
| library(glue) | |
| setwd("~/Documents/bioinformatics/") | |
| ids <- read_excel("NCTC_pacbio.xlsx", col_names = c("strains", "run_acc")) %>% | |
| mutate(run_acc = gsub("https://www.ebi.ac.uk/ena/data/view/", "", run_acc)) %>% | |
| mutate(run_acc_url = glue("https://www.ebi.ac.uk/ena/data/warehouse/filereport?accession={run_acc}&result=read_run&fields=run_accession,submitted_ftp,submitted_md5")) |
| library(readr) | |
| library(dplyr) | |
| add.alpha <- function(col, alpha=1){ | |
| if(missing(col)) | |
| stop("Please provide a vector of colours.") | |
| apply(sapply(col, col2rgb)/255, 2, | |
| function(x) | |
| rgb(x[1], x[2], x[3], alpha=alpha)) | |
| } |
| library(RSelenium) | |
| library(dplyr) | |
| library(rvest) | |
| library(tibble) | |
| #add url | |
| url <- "https://www.toimitilat.fi/toimitilahaku/?size_min=&size_max=&deal_type%5B%5D=1&language=fin&result_type=list&advanced=0&gbl=1&ref=main#searchresult" | |
| # docker run -d -p 4445:4444 selenium/standalone-firefox:2.53.1 | |
| remDr <- remoteDriver( | |
| remoteServerAddr = "127.0.0.1", |
| #!/usr/bin/env nextflow | |
| params.pattern = "*_L001_R{1,2}_001.fastq.gz" | |
| params.input = "/hpc-home/leviet/data/gonococci/July13" | |
| params.output = "/hpc-home/leviet/data/gonococci_result_July13" | |
| params.readlen = 150 | |
| params.db = "/qib/platforms/Informatics/databases/kraken2/kraken2_db_20190110" | |
| params.bracken_kmer = "/qib/platforms/Informatics/databases/bracken/database150mers.kmer_distrib" | |
| params.tax_level = "S" | |
| threads = 8 |
SAM and BAM filtering one-liners
@author: David Fredman, [email protected] (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/
Please extend with additional/faster/better solutions via a pull request!
BWA mapping (using piping for minimal disk I/O)
| library(ape) | |
| tree <- rtree(n = 20) | |
| plot(tree, edge.width = 2) | |
| #By default, tips odered from bottom to top | |
| t <- tree$tip.label | |
| # Re order from top to bottom | |
| rev(tree$tip.label) | |
| #Write out to a text file | |
| sapply(t, function(x) write(x,"tips.txt", append = T)) |
| mtcars %>% | |
| mutate( | |
| selected = case_when( | |
| cyl == 6 & carb == 4 ~ "yes", | |
| cyl == 8 & carb == 8 ~ "yes", | |
| TRUE ~ "no" | |
| ) | |
| ) %>% | |
| filter(selected == "yes") %>% | |
| select(-selected) |
