Jeffrey jvwong

## crossref_query.sh
QUERY="Inositol pyrophosphate dynamics reveals control of the yeast PHO starvation program through 1,5-IP8 and the SPX domain of Pho81"
curl --get --data-urlencode "query.bibliographic=${QUERY}" "https://api.crossref.org/works/?filter=type:journal-article,type:posted-content&rows=1" | jq '. | { title: .message.items[0].title[0], abstract: .message.items[0].abstract, doi: .message.items[0].DOI, publisher: .message.items[0].publisher }'

## renew.sh
certbot certonly --webroot --webroot-path=<webroot path> --cert-name <certname> -d <domain>

## parse_dotenv.bash
# Pass the env-vars to MYCOMMAND
eval $(egrep -v '^#' .env | xargs) MYCOMMAND
# … or ...
# Export the vars in .env into your shell:
export $(egrep -v '^#' .env | xargs)

## feeds.xml
<?xml version="1.0" encoding="UTF-8"?>

<opml version="1.0">
    <head>
        <title>Ross's academic journal RSS feed subscriptions</title>
    </head>
    <body>
        <outline text="General Biology Journals" title="General Biology Journals">
            <outline type="rss" text="BioEssays" title="BioEssays" xmlUrl="http://onlinelibrary.wiley.com/rss/journal/10.1002/(ISSN)1521-1878" htmlUrl="http://onlinelibrary.wiley.com/resolve/doi?DOI=10.1002%2F%28ISSN%291521-1878"/>
            <outline type="rss" text="Biol J Linn Soc" title="Biol J Linn Soc" xmlUrl="http://onlinelibrary.wiley.com/rss/journal/10.1111/(ISSN)1095-8312" htmlUrl="http://onlinelibrary.wiley.com/resolve/doi?DOI=10.1111%2F%28ISSN%291095-8312"/>

## cmd_line_opts.sh
#!/bin/bash

dflag=
iflag=
oflag=
while getopts 'dio:' OPTION
do
  case $OPTION in
    d)  dflag=1
        ;;

## grep_row_table.sh
#!/bin/bash
# Find row and print columns in tab-delimited file

#tax_id	GeneID	PubMed_ID
tax_id=9606
GeneID=9518

grep -Ei "^$tax_id\t$GeneID\t[0-9.]+$" ./data/gene2pubmed > result.txt

## faketimeout.js
const TIMEOUT = 5000;

const promiseTimeout = delay => new Promise( ( resolve, reject ) =>  setTimeout( () => reject( new Error('fake timeout') ), delay ) );


const doSomethingAsync =  ( ) => {
  return Promise.resolve()
    .then( () => promiseTimeout( TIMEOUT ) );
};

## fishers.R
# Probability of GO term (GeneSet) in gene hits (Hits) from a screen

# Initialize our relevant variables
nBackground     <- 407 # Total genes screened
nGeneSet        <- 18  # Genes in GO term that are in the bachground
nHits           <- 60  # Genes enriched in screen in background
nOutsideGeneSet <- nBackground - nGeneSet  # Genes not in GeneSet but in background
nQueryPathway   <- 0:nGeneSet # Overlap between query genes ('Hits') and GO term (in background)

# Use the dhyper built-in function for hypergeometric probability

## enrichment.js
// const request = require('request');
// const Promise = require('promise-simple');
// const csv = require('csvtojson');
// const fs = require('fs');
// const _ = require('lodash');
const enrichment = function (query) {

  var promise = new Promise(function(resolve, reject) {
    // do a thing, possibly async, then…


## gprofiler.js
var request = require('request');

var formData = {
  "output": "mini",
  "organism": "hsapiens",
  "significant": "1",
  "sort_by_structure": "1",
  "ordered_query": "0",
  "as_ranges": "0",
  "no_iea": "1",
	QUERY="Inositol pyrophosphate dynamics reveals control of the yeast PHO starvation program through 1,5-IP8 and the SPX domain of Pho81"
	curl --get --data-urlencode "query.bibliographic=${QUERY}" "https://api.crossref.org/works/?filter=type:journal-article,type:posted-content&rows=1" \| jq '. \| { title: .message.items[0].title[0], abstract: .message.items[0].abstract, doi: .message.items[0].DOI, publisher: .message.items[0].publisher }'
	# Pass the env-vars to MYCOMMAND
	eval $(egrep -v '^#' .env \| xargs) MYCOMMAND
	# … or ...
	# Export the vars in .env into your shell:
	export $(egrep -v '^#' .env \| xargs)
	<?xml version="1.0" encoding="UTF-8"?>

	<opml version="1.0">
	<head>
	<title>Ross's academic journal RSS feed subscriptions</title>
	</head>
	<body>
	<outline text="General Biology Journals" title="General Biology Journals">
	<outline type="rss" text="BioEssays" title="BioEssays" xmlUrl="http://onlinelibrary.wiley.com/rss/journal/10.1002/(ISSN)1521-1878" htmlUrl="http://onlinelibrary.wiley.com/resolve/doi?DOI=10.1002%2F%28ISSN%291521-1878"/>
	<outline type="rss" text="Biol J Linn Soc" title="Biol J Linn Soc" xmlUrl="http://onlinelibrary.wiley.com/rss/journal/10.1111/(ISSN)1095-8312" htmlUrl="http://onlinelibrary.wiley.com/resolve/doi?DOI=10.1111%2F%28ISSN%291095-8312"/>
	#!/bin/bash

	dflag=
	iflag=
	oflag=
	while getopts 'dio:' OPTION
	do
	case $OPTION in
	d) dflag=1
	;;
	#!/bin/bash
	# Find row and print columns in tab-delimited file

	#tax_id GeneID PubMed_ID
	tax_id=9606
	GeneID=9518

	grep -Ei "^$tax_id\t$GeneID\t[0-9.]+$" ./data/gene2pubmed > result.txt
	const TIMEOUT = 5000;

	const promiseTimeout = delay => new Promise( ( resolve, reject ) => setTimeout( () => reject( new Error('fake timeout') ), delay ) );


	const doSomethingAsync = ( ) => {
	return Promise.resolve()
	.then( () => promiseTimeout( TIMEOUT ) );
	};
	# Probability of GO term (GeneSet) in gene hits (Hits) from a screen

	# Initialize our relevant variables
	nBackground <- 407 # Total genes screened
	nGeneSet <- 18 # Genes in GO term that are in the bachground
	nHits <- 60 # Genes enriched in screen in background
	nOutsideGeneSet <- nBackground - nGeneSet # Genes not in GeneSet but in background
	nQueryPathway <- 0:nGeneSet # Overlap between query genes ('Hits') and GO term (in background)

	# Use the dhyper built-in function for hypergeometric probability
	// const request = require('request');
	// const Promise = require('promise-simple');
	// const csv = require('csvtojson');
	// const fs = require('fs');
	// const _ = require('lodash');
	const enrichment = function (query) {

	var promise = new Promise(function(resolve, reject) {
	// do a thing, possibly async, then…
	var request = require('request');

	var formData = {
	"output": "mini",
	"organism": "hsapiens",
	"significant": "1",
	"sort_by_structure": "1",
	"ordered_query": "0",
	"as_ranges": "0",
	"no_iea": "1",