astatham

#!/bin/bash
#Important notes
#if backupdir is under homedir then backupdir must be included in the "$backupdir"/exclude file otherwise it will recurse
#also "$backupdir"/exclude file must not contain blank lines (match everything therefore backup nothing)
homedir="/home/aarsta"
backupdir="/home/aarsta/R_Backup"

find "$homedir" -name "*.R" | grep -v -f "$backupdir"/exclude | grep -o \\/.*\\/ | sort | uniq | sed -e "s%"$homedir"/%"$backupdir"/%" -e 's% %_%g'| xargs mkdir -p

SAVEIFS=$IFS

astatham

cufflinks2TranscriptDB <- function(filename, verbose=TRUE) {

    require(rtracklayer)
    require(GenomicRanges)
    require(GenomicFeatures)

    requiredAttribs <- c("gene_id", "transcript_id", "exon_number")

    if (verbose) message("Importing ", filename)
    tmp <- import.gff(filename, asRangedData=FALSE)

astatham

GpCplot <- function(amplicon, reads, main="", minScore=150) {
  require(Biostrings)
  require(GenomicRanges)
  if (class(amplicon)=="character") amplicon <- DNAString(amplicon)
  amplicon.conv <- DNAString(gsub("C", "T", gsub("GC", "GY", gsub("CG", "YG", amplicon))))
  reads <- read.DNAStringSet(reads)
  readsHitAll <- list("plus"=pairwiseAlignment(reads, amplicon.conv, type="local-global"), "minus"=pairwiseAlignment(reverseComplement(reads), amplicon.conv, type="local-global"))
  
  readsStrand <- ifelse(score(readsHitAll$plus)>score(readsHitAll$minus), "+", "-")
  reads2 <- reads

astatham

lboxplot <- function(x, cols=2:(length(x)+1), ...) {
    xl <- length(x)
    if (xl<2) stop("Length of x must be >=2")
    xn <- sapply(x, length)
    if (!all(xn==xn[1])) stop ("Element lengths of x must all be the same")
    xnames <- sapply(x, names)
    if (!all(apply(xnames, 1, function(y) all(y==y[1])))) stop("Each element of x must have matching names")
    xn <- xn[1]
    xu <- unlist(x, recursive=FALSE)[rep(1:xn, each=xl)+rep((1:xl-1)*xn, xn)]
    boxplot(xu, col=cols, xaxt="n", ...)

astatham

plotDensities <- function(s, col=NULL, xlim=NULL, ylim=NULL, na.rm=TRUE, lty=rep(1, length(s)), ...) {
    if (!is.list(s)) s <- list(s)
    if (is.null(col)) col <- rainbow(length(s))
    sD <- lapply(s, density, na.rm=na.rm)
    if (is.null(xlim)) xlim <- range(sapply(sD, function(x) range(x$x)))
    if (is.null(ylim))ylim <- range(sapply(sD, function(x) range(x$y)))
    plot(0, type="n", xlim=xlim, ylim=ylim, ...)
    for (i in 1:length(sD)) lines(sD[[i]], col=col[i], lty=lty[i], ...)
}

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

#!/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

JIRAtable <- function(x) {
    message(paste0("||", paste(names(x), collapse="||"), "||"))
    for (i in 1:nrow(x)) message(paste0("|", paste(sapply(x[i,], as.character), collapse="|"), "|"))
}