How to...

Matt

How to filter mapped/unmapped fastq reads:

get all the reads where both mapped:

samtools view -F 12 bothEndsMapped.bam

get all the reads that did not map, but whose mate mapped:

samtools view  -F 4 -f 8 onlyThisEndMapped.bam

get all the reads that mapped, but whose mates did not:

samtools view -F 8 -f 4 onlyThatEndMapped.bam

get all the reads where neither one mapped:

samtools view -f 12 neitherEndMapped.bam

Matt

How to write nodejs async/await code:

// With function declaration
async function myFn() {
  // await ...
}
// With arrow function
const myFn = async () => {
  // await ...
}

Source

Matt

How to display the contents of a circular JSON object in nodejs:

Method1:

		const getCircularReplacer = () => {
		  const seen = new WeakSet();
		  return (key, value) => {
		    if (typeof value === "object" && value !== null) {
		      if (seen.has(value)) {
		        return;
		      }
		      seen.add(value);
		    }
		    return value;
		  };
		};

		var string=JSON.stringify(circularJSONobject, getCircularReplacer());
		console.log(string);

Method 2:

var util = require('util'); //a core nodejs function but it has to be imported
console.log(util.inspect(circularJSONobject));

Matt

How to create post buttons that look like links:

css:

  .link-button {
    background: none;
    border: none;
    color: #337ab7;
    cursor: pointer;
    font-size: 19px;
    font-weight: 400;
    font-family: 'Lato', sans-serif;
  }
  .link-button:focus {
    outline: none;
  }
  .link-button:active {
    color:red;
  }
  .link-button:hover {
    text-decoration: underline;
    filter: brightness(65%);
  }

html:

<form method="post" action="https://mics.com/index" class="inline">
<button type="submit" name="submit_name" value="name" class="link-button">link display text</button>
</form>

Matt

How to display line numbers for pasted code in NodeBB:

This is from here.

NB. (This isn't working for me)

Put this in your custom header (ACP -> Appearance -> Custom HTML & CSS -> Custom Header):

<script>
require(['highlight'], function (hljs) {
  require([
    'https://cdnjs.cloudflare.com/ajax/libs/highlightjs-line-numbers.js/1.1.0/highlightjs-line-numbers.min.js'
  ], function () {
    $(window).on('load action:ajaxify.end', function () {
      setTimeout(function () {
        hljs.initLineNumbersOnLoad();
      }, 100);
    });
  });
});
</script>

NB. The contents of 'highlightjs-line-numbers.min.js' are:

!function(e){"use strict";function t(){"complete"===document.readyState?n():e.addEventListener("DOMContentLoaded",n)}function n(){try{var e=document.querySelectorAll("code.hljs");for(var t in e)e.hasOwnProperty(t)&&r(e[t])}catch(n){console.error("LineNumbers error: ",n)}}function r(e){if("object"==typeof e){var t=e.parentNode,n=o(t.textContent);if(n>1){for(var r="",c=0;n>c;c++)r+=c+1+"\n";var l=document.createElement("code");l.className="hljs hljs-line-numbers",l.style["float"]="left",l.textContent=r,t.insertBefore(l,e)}}}function o(e){if(0===e.length)return 0;var t=/\r\n|\r|\n/g,n=e.match(t);return n=n?n.length:0,e[e.length-1].match(t)||(n+=1),n}"undefined"==typeof e.hljs?console.error("highlight.js not detected!"):(e.hljs.initLineNumbersOnLoad=t,e.hljs.lineNumbersBlock=r)}(window);

Matt

How to cycle/loop through an object in javascript:

for (var key in req.body) {
    if (key in req.body) {
        console.log(req.body[key]);
    }
}

Matt

%(#ffffff)[How to publish a package with npm:]

*Sign in with npm login:

npm login

You’ll be prompted to enter your username, password, and email address.

*Create a folder named how-to-publish-to-npm:

mkdir how-to-publish-to-npm

*Navigate into the folder:

cd how-to-publish-to-npm

*Begin the project with the npm init command:

npm init

This command runs you through a few questions and creates a package.json file for you at the end. This package.json file contains the bare necessities you need to publish your project. (Feel free to skip questions that don’t make sense).

*The final step is to publish your package with the npm publish command:

npm publish

Matt

How to set permissions in linux with chmod:

chmod 600 {filespec}	You can read and write; the world can't. Good for files.
chmod 700 {filespec}	You can read, write, and execute; the world can't. Good for scripts.
chmod 644 {filespec}	You can read and write; the world can only read. Good for web pages.
chmod 640 {filespec}	You can read and write; group can read, the world can't do anything.Good for group project..
chmod 755 {filespec}	You can read, write, and execute; the world can read and execute. Good for programs you want to share, and your public_html directory.
chmod 750 {filespec}	You can read, write, and execute; the group can read and execute, the world can't do anything. Good for programs you want to share within group.

Matt

How to install WebODM on Windows 10 home:

Download Docker Toolbox and install it as an administrator. (You may need to uninstall VirtualBox first.)
Launch Docker Quickstart Terminal as an administrator. Note down the IP address shown below the whale.


                        ##         .
                  ## ## ##        ==
               ## ## ## ## ##    ===
           /"""""""""""""""""\___/ ===
      ~~~ {~~ ~~~~ ~~~ ~~~~ ~~~ ~ /  ===- ~~~
           \______ o           __/
             \    \         __/
              \____\_______/

docker is configured to use the default machine with IP 192.168.99.100
For help getting started, check out the docs at https://docs.docker.com

Download WebODM with Git and start it:

git clone https://github.com/OpenDroneMap/WebODM --config core.autocrlf=input --depth 1
cd WebODM
sh ./webodm.sh start

Navigate to port 8000 of the IP address recorded in the first step:

http://192.168.99.100:8000

It is advisable to resize the VM associated with WebODM.

cd "C:\Program Files\Oracle\VirtualBox"
./VBoxManage clonemedium disk --format VDI "C:\Users\username\.docker\machine\machines\default\disk.vmdk" "C:\Users\username\.docker\machine\machines\default\disk.vdi"

./VBoxManage modifyhd "C:\Users\username\.docker\machine\machines\default\disk.vdi" --resize 100000

After resizing you will need to use a GParted VM to resize the partitions.

If you want to stop WebODM then use the command:

sh ./webodm.sh down

To completely stop WebODM you will have to also stop the VirtualBox VBoxHeadless process using the Windows task manager

Matt

How to pipe output from a shell command to Perl to a shell command within a Perl script:

$com='samtools view -h '.$infile;
my $zom='samtools view -bS - > q64converted.bam';
open(SBAM, "$com|");
open SBOUT, "|$zom";
while (<SBAM>){
	print SBOUT "$_";
}
close(SBAM);
close SBOUT;

Matt

How to find out which pages are visited according to user country in Google Analytics:

how to view visited pages by country.jpg

Matt

How to horizontally split a file view in sublime text editor:

Split the view by using View -> Layout -> Rows: 2. Then select Row 1 and go to File -> New View into File. It will open second tab with the same file. Then you can drag that tab to the Row 2.

Matt

How to push a docker image to Docker Hub:

You need to have an account on Docker Hub. In this example the account is named 'ning'.
The image must be built so that the account name is within the image name

Eg. for docker command:

docker tag nextflow_docker:202004201512  ning/nextflow_docker:202004201512

For a docker-compose file:

version: '3'
services:
  nextflow_docker:
    build: ./nextflow_docker
    image: ning/nextflow_docker:latest

Then you need to push:

docker logout
docker login
#login with your username and password (if you are on ubuntu you can ignore password keyring (agree but dont enter a password)
#NB. If you are on ubuntu and get the error message "Error calling StartServiceByName for org.freedesktop.secrets: Timeout was reached" , try the following command "sudo apt remove gnome-keyring golang-docker-credential-helpers"
docker push ning/nextflow_docker:latest

Matt

How to translate a singularity recipe into a Dockerfile:

First install spython:

git clone https://www.github.com/singularityhub/singularity-cli.git
cd singularity-cli
python3 setup.py install

Then perform the conversion:

spython recipe /input/path/to/singularity/recipe/Singularity /output/path/to/Dockerfile

Matt

How to resize the left and right padding in large screens with CSS. (NB. Probably better to use bootstrap with 3 columns instead):

In the head section:

<head>
  <meta name="viewport" content="width=device-width, initial-scale=1.0">

  <style>   
    @media screen and (min-width: 768px) {
        body {
            padding-left: 100px;
            padding-right: 100px;
        }
    }
  </style>

</head>

Matt

How to horizontally write the address on an envelope in Japan:

〒106-0044東京都港区東麻布1-8-1 ISビル4F GPlusMedia

Matt

How to find the meanings of symbols in R:

?"@"
?"[["

Matt

How to overcome the following error message in Rstudio:

WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

In the R console:

#Find where Rtools is installed:
Sys.which("make")

#Find where .Rprofile or .Rprofile.site is (my .Rprofile.site was in C:\R\R-3.6.2\etc):
Sys.getenv("HOME")

Add these two lines to .Rprofile.site (or .Rprofile):

Sys.setenv(PATH = paste("C:/rtools40/usr/bin", Sys.getenv("PATH"), sep=";"))
Sys.setenv(BINPREF = "C:/rtools40/mingw_$(WIN)/bin/")

Matt

How to use caret library from R to create folds for k-fold validation:

# Import caret
library(caret)
# 10-Fold cross validation
valid_sets = createFolds(1:nrow(data), k = 10)

How to create a vector with 10 zeroes in R:

vector = numeric(length(1:10))

Matt

How to find the most common element in a vector in R:

mostCommon <- function(x){
     un <- unique(x)
     un[which.max(tabulate(match(x,un)))]
}