nathandunn’s gists

nathandunn / converter.js

Last active September 20, 2019 20:07

tsv to json converter

	function tsvJSON(tsv){
	var lines=tsv.split("\n");
	var result = [];
	for(var i=0;i<lines.length;i++){
	var obj = {};
	var currentline=lines[i].split("\t");
	if(currentline.length>2){
	obj.gene = currentline[1].split(",");
	if(currentline[0].indexOf('(GO:')>0){
	const startIndex = currentline[0].indexOf('(GO:');

nathandunn / Bioschemas Example 3

Last active October 29, 2018 19:19

Example of a proposed bioschemas example

	{
	"@context": [
	"http://schema.org",
	"http://bioschemas.org/context.jsonld"
	],
	"@id": "http://www.alliancegenome.org/gene/ZFIN:ZDB-GENE-001103-2",
	"@type": ["BioChemEntity", "Gene"],
	"identifier": "ZFIN:ZDB-GENE-001103-2",
	"version": "1.8",
	"license": "CC BY 4.0",

nathandunn / gist:9f1a31b5c54e06edc2ef35339911e2e7

Created June 6, 2018 21:31

failing query

	```(; datasetFetch
	(fn [dataset samples probes]
	(fetch [{:table dataset
	:columns probes
	:samples samples}]))
	"ccle/CCLE_DepMap_18Q2_maf_20180502" ["127399_SOFT_TISSUE" "22RV1_PROSTATE" "A204_SOFT_TISSUE" "A253_SALIVARY_GLAND" "A427_LUNG" "A431_SKIN" "A4FUK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE" "A673_BONE" "ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE" "BICR16_UPPER_AERODIGESTIVE_TRACT" "BICR78_UPPER_AERODIGESTIVE_TRACT" "BIN67_OVARY" "BT12_SOFT_TISSUE" "BT16_SOFT_TISSUE" "C10_LARGE_INTESTINE" "C125PM_LARGE_INTESTINE" "C75_LARGE_INTESTINE" "C80_LARGE_INTESTINE" "C8166_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE" "C84_LARGE_INTESTINE" "C99_LARGE_INTESTINE" "CADOES1_BONE" "CAKI2_KIDNEY" "CALU1_LUNG" "CCFSTTG1_CENTRAL_NERVOUS_SYSTEM" "CHLA06ATRT_SOFT_TISSUE" "CHLA15_AUTONOMIC_GANGLIA" "CHLA218_BONE" "CHLA258_BONE" "CHLA266_SOFT_TISSUE" "CHLA32_BONE" "CHLA57_BONE" "CHLA99_BONE" "CHLA9_BONE" "CL11_LARGE_INTESTINE" "CME1_SOFT_TISSUE" "COGAR359_SOFT_TISSUE" "COGE352_BONE" "COGN278_AUTONOMIC_GANGLIA" "COGN3

nathandunn / overview-plugin.html

Created March 28, 2017 22:31

like overview.html, but trying to add the neatfeatures plugin

	<html>
	<head>
	<title>JBrowse - Retrieve data outside of browser</title>

	<link rel="stylesheet" type="text/css" href="css/genome.css">
	<script type="text/javascript" src="src/dojo/dojo.js" data-dojo-config="async: 1, baseUrl: './src'"></script>
	<script type="text/javascript" src="src/JBrowse/init.js"></script>
	<style>
	pre {
	white-space: pre-wrap;

nathandunn / overview.html

Created March 28, 2017 19:12

provides an overview screenshot from a remote JBrowse source specified in URL

	<html>
	<head>
	<title>JBrowse - Retrieve data outside of browser</title>

	<link rel="stylesheet" type="text/css" href="css/genome.css">
	<script type="text/javascript" src="src/dojo/dojo.js" data-dojo-config="async: 1, baseUrl: './src'"></script>
	<script type="text/javascript" src="src/JBrowse/init.js"></script>
	<style>
	pre {
	white-space: pre-wrap;

nathandunn / jbrowse-render

Created March 13, 2017 17:55 — forked from cmdcolin/jbrowse-render

JBrowse feature rendering outside browser

	<html>
	<head>
	<title>JBrowse feature rendering outside of browser</title>

	<link rel="stylesheet" type="text/css" href="css/genome.css">
	<script type="text/javascript" src="src/dojo/dojo.js" data-dojo-config="async: 1, baseUrl: './src'"></script>
	<script type="text/javascript" src="src/JBrowse/init.js"></script>

	<script>

nathandunn / features.html

Last active January 31, 2017 18:14

Grabs nclist from remote and local server data

	<!DOCTYPE html>
	<html>
	<head>
	<title>JBrowse - Retrieve data outside of browser</title>
	<meta content="text/html;charset=utf-8" http-equiv="Content-Type">
	<link rel="stylesheet" type="text/css" href="css/genome.css">
	<script type="text/javascript" src="src/dojo/dojo.js" data-dojo-config="async: 1, baseUrl: './src'"></script>
	<script type="text/javascript" src="src/JBrowse/init.js"></script>
	<style>
	pre {

nathandunn / screenshot.py

Last active January 27, 2017 18:36

simple python JBrowse extraction

	from selenium import webdriver
	from selenium.webdriver.common.by import By
	from selenium.webdriver.support.ui import WebDriverWait
	from selenium.webdriver.support import expected_conditions as EC

	import cv2
	url = 'https://genome.monarchinitiative.org/apollo/Honeybee/jbrowse/index.html?loc=Group1.1%3A724016..726600&tracklist=0&nav=0&tracks=Official%20Gene%20Set%20v3.2&highlight='

	driver = webdriver.Chrome()
	driver.get(url)

nathandunn / gist:3cc00bdae00635b4733e7b4566610489

Created October 13, 2016 03:58

sequence strings for difference frames

Frame 1 longest:

TCCGGAACAACGAAGATGAGATGGGATGCCGCTCTATATCTACTCTCGCTGCTGCTCTTCTCGTTGGCCAATCTGTGTTGGGCTCTCGTCGAAACGCGAGGATGCAATCGCACTATCAGAAATTCCGTTGGATGGATACGTTGGACAGGACGAATGGGACGATGCATTGTTCGCATCAGAGCGCCTCCTAGAGATCCTCAGGTGATCGAGTTGAAAGTTAGGAAACTGCAAGTTGGTTTCCTGAAAGAAACCAGATGCGAGGGTGCTTACATTCAATTTTCCGATGGTAGCGAGGACCTTGAAGATGAAACGGGACGTTACTGCGGCTATGTAAGCGGCAACACGACCAGACTGTTCCTGAGAAAGGGACCCAATTTGACGATCATAATGGACTCGGACGTGAGGTTCGCAGCCGAGAATCCCGTGATATTCTCCGCCCAGTTCTCCATACTTCCCGCCCAGCTCGCGTCCGAGCGTCACCGCGGCTTCTCCCCGTCCCCCTCGTCCGAGTGTCCCCTCGAGTGCGCCGTGAGGAACGAGCGAAGATCCTGCAAATTGTCCTCGCCCGGCTACCCGGGCGTCTACCCCCGCGGGATCAAGTGCAGGATAGGGTTGGAGTCGGGCGCCGGCCGATTCAAGATCGGCGGCCAACCGGACGACACTTACGATCTGATGAATCGCACGTGGCAGGAGGGTTGCCAGACCGAGAATTGCGAGGACCACGTGGAGGGGATGGTCGCGGAATTGCGGAGGGCGAGGGTCGAGCCGGGGGACGCGGGGAGGCGCGGGAAGAGGAGCCCGGAGGACCGCGAGGAGGAGGTGGAGTTTATCATCGGGCAGACGTCGTACAGGGGGGGTAGGAATGGTCGGAGGAGGCTTAAGAAGGGGAGGAAGGATGCCGGGAGCGAGGATATCCGGAGAGGAAACATCGGCCGGGCGAAGGGGGGTGGGGAGGGAGGAGAGTCGTTGGCCGGTTATCGGGGGGGCCAGGGGATCAGGTGGCGGG

nathandunn / FeatureSet.java

Created October 12, 2016 00:06

original desktop apollo featureset code

	package apollo.datamodel;

	import java.lang.Integer;
	import java.util.*;
	import javax.swing.JOptionPane;

	import apollo.util.SeqFeatureUtil;
	import apollo.util.FeatureList;
	import apollo.util.QuickSort;

Nathan Dunn nathandunn