thoukydides

// Variables used by Scriptable.
// These must be at the very top of the file. Do not edit.
// icon-color: green; icon-glyph: trash-alt;
// South Cambridgeshire bin collection widget from iOS Scriptable
// Copyright © 2020 Alexander Thoukydides

'use strict';

// South Cambridgeshire District Council API configuration
// (reverse engineered from https://www.scambs.gov.uk/Scripts/bin-calendar.js)

cadriel

Plate layout

["~\n`","!\n1","@\n2","#\n3","$\n4","%\n5","^\n6","&\n7","*\n8","(\n9",")\n0","_\n-","+\n=",{w:2},"Backspace",{a:7},""],
[{a:4,w:1.5},"Tab","Q","W","E","R","T","Y","U","I","O","P","{\n[","}\n]",{w:1.5},"|\n\\",{a:7},""],
[{w:1.25}, "Stepped", {a:4,w:1.75, x:-1.25},"Caps Lock","A","S","D","F","G","H","J","K","L",":\n;","\"\n'",{w:2.25},"Enter",{a:7},""],
[{a:4,w:2.25},"Shift","Z","X","C","V","B","N","M","<\n,",">\n.","?\n/",{w:1.75},"Shift",{a:7},"",""],
[{a:4,w:1.25},"Ctrl",{w:1.25},"Win",{w:1.25},"Alt",{a:7,w:6.25,_rs:180},"",{a:4,w:1.5},"Alt",{w:1.5},"Win","Menu","Ctrl",{a:7},""]

Custom Polygons, centered on [-x,y]

darencard

Extracting spliced sequences (e.g., CDS) from GFF files

GFF is a common format for storing genetic feature annotations. In the case of gene annotations, subsets of elements are split over multiple lines, as things like exons and CDS features will have gaps based on the full genome sequence. Therefore, while it is easy to extract exon and CDS lines, it can be difficult to associate them together based on a parent (e.g., transcript) ID and perform downstream operations. Even extracting the full CDS sequence using a GFF file can be tricky for this reason, even though it seems trivial.

Here we'll overcome this difficulty using the gffread tool. Installation is pretty easy and is documented in the GitHub README. gffread has a lot of options, but here we'll just document one that extracts the spliced CDS for each GFF transcript (-x option). Note that you can do the same thing for exons (-w option) and can also produce the protein sequence (-y option).

Let's extra

lewisridden

[
  {
    "name": "Iris Keyboard",
    "author": "Lewis Ridden"
  },
  [
    {
      "x": 3,
      "c": "#c4c8c5",
      "a": 5

adam-garcia

Viridis Color Palette Generator

A simple tool for extracting discrete color palette values from the viridis collection of color palettes.

devhero

Byobu is a suite of enhancements to tmux, as a command line
tool providing live system status, dynamic window management,
and some convenient keybindings:

  F1                             * Used by X11 *
    Shift-F1                     Display this help
  F2                             Create a new window
    Shift-F2                     Create a horizontal split
    Ctrl-F2                      Create a vertical split
    Ctrl-Shift-F2                Create a new session

daler

"""
https://www.biostars.org/p/152517/

Example of how to work with Ensembl release 81 GTF files, which:

    1) already have genes and transcripts included

    2) have unique IDs for genes, transcripts, and exons in the corresponding
       "<featuretype>_id" attribute

nztim

###Install Node and Bower

• Set up the NodeSource repo and install Node
• curl -sL https://deb.nodesource.com/setup_0.12 | sudo bash -
• sudo apt-get install nodejs
• Install bower: sudo npm install -g bower

Install StackEdit

• Clone the repo: git clone https://github.com/benweet/stackedit
• To use a domain other than 'localhost', edit /public/res/constants.js:
• constants.BASE_URL = "http://stackedit.dev:3000/";

davetang

#!/usr/bin/env perl

use strict;
use warnings;

=head1 NAME

This scripts converts a psl file into a bed file written by Dave Tang.

=head1 SYNOPSIS

ssstonebraker

FILE SPACING:

 # double space a file
 sed G

 # double space a file which already has blank lines in it. Output file
 # should contain no more than one blank line between lines of text.
 sed '/^$/d;G'