astatham

# wolfpack modules required: hugfre/R/3.0.2 fabbus/aspera/3.1.1.70290
 
ascpCMD <- "ascp -QT -l1000M -i /share/ClusterShare/software/contrib/fabbus/aspera/3.1.1.70290/asperaweb_id_dsa.putty"
 
library(SRAdb)
if (!file.exists("../SRAmetadb.sqlite")) db <- getSRAdbFile("../") else db <- "../SRAmetadb.sqlite"
con <- dbConnect(dbDriver("SQLite"), db) # load the SRA database
 
accession <- "SRP026604"
 

astatham

// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console

astatham

CREATE TABLE log(
    time TEXT TEXT,    
    account TEXT TEXT,    
    env_list TEXT,    
    gid TEXT,    
    grp TEXT,    
    job_name TEXT,    
    job_number TEXT,    
    jobshare TEXT,    
    mail_list TEXT,    

astatham

library(rjson)
options(scipen=10000)
if (file.exists("IAMA.db")) file.remove("IAMA.db")
system("sqlite3 IAMA.db < IAMA_scraper.schema;")

while (TRUE) {

    bigTab <- NULL
    after <- ""
    baseURL <- "http://www.reddit.com/r/iama/.json?sort=new&limit=100"

astatham

imguRupload <- function(filename, title=NULL, caption=NULL, name=basename(filename), apikey="4feb29d00face5bc1b9dae536e15c373") {
    require(RCurl)
    require(RJSONIO)
    if (length(filename)>1) stop("'filename' must be length 1.")
    if (!file.exists(filename)) stop(filename, "does not exist!")
    params <- list(key=apikey, image=fileUpload(filename), name=filename)
    if (!is.null(title)) params[["title"]] <- title
    if (!is.null(caption)) params[["caption"]] <- caption
    fromJSON(rawToChar(postForm("http://api.imgur.com/2/upload.json", .params=params)))$upload
}

astatham

imguRupload <- function(filename, title=NULL, caption=NULL, name=basename(filename), apikey="4feb29d00face5bc1b9dae536e15c373") {
    require(RCurl)
    require(RJSONIO)
    if (length(filename)>1) stop("'filename' must be length 1.")
    if (!file.exists(filename)) stop(filename, "does not exist!")
    params <- list(key=apikey, image=fileUpload(filename), name=filename)
    if (!is.null(title)) params[["title"]] <- title
    if (!is.null(caption)) params[["caption"]] <- caption
    fromJSON(rawToChar(postForm("http://api.imgur.com/2/upload.json", .params=params)))$upload
}

astatham

#!/usr/local/bin/Rscript
library(twitteR)
library(imguR)
sess <- initSession("clark_lab_linux", "password")
rstats <- searchTwitter("#rstats", sess, n=1000)
#filter out junk
rstats <- rstats[sapply(sapply(rstats, screenName), length)>0]

#make graph
posters <- sort(table(sapply(rstats, screenName)), decreasing=TRUE)

astatham

#!/bin/bash -e

if [[ ! -f "${1}" ]] ; then
    echo "File $1 does not exist, aborting."
    exit 1
fi
# Replace double digit chromosomes first
cmd="sed"
for i in `seq 10 22` `seq 1 9` X Y; do
    cmd="$cmd -e 's/chr$i/$i/g'"

astatham

#!/usr/bin/perl -w
#
# script for nagios notify via Jabber / Google Talk Instant Messaging
#   using XMPP protocol and SASL PLAIN authentication.
#
# author: Andrew Elwell <A.Elwell@physics.gla.ac.uk>
# based on work by Thus0 <Thus0@free.fr> and  David Cox
#
# released under the terms of the GNU General Public License v2
# Copyright 2007 Andrew Elwell.

astatham

> 2:3 %in% 1:5
[1] TRUE TRUE
> !2:3 %in% 1:5
[1] FALSE FALSE