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library(IRanges)
library(httr)
library(jsonlite)

version <- '0.3'

collapse <- function(...) {
    paste(unlist(list(...)), sep=",", collapse=",")
}

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library(limma)
library(Matrix)

## Create the experimental variables and put them in a data frame
animal <- factor(rep(sprintf("Animal %s", 1:6), each=2))
timep <- factor(c("Pre", "Post"), levels=c("Pre", "Post"))
treat <- factor(c("control", "control", "reagent", "reagent"))
df <- data.frame(animal, timep, treat)
df$replicate <- as.numeric(droplevels(df$animal:df$timep:df$treat))
## Create technical replicates by duplicating each row

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#!/bin/bash

#$ -cwd
#$ -l jabba,mem_free=10G,h_vmem=2G,h_fsize=1G 
#$ -N approach1b
#$ -pe local 20
#$ -m e

echo "**** Job starts ****"
date

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library(codetools)

getNonPackageVars <- function (pos=-1L, envir=as.environment(pos)) {
    npvarnames <- c()
    while (TRUE) {
        if (identical(envir, emptyenv()) ||
            identical(envir, .BaseNamespaceEnv)) {
            ## If we hit the empty env, then we started in a package
            ## namespace, so there are no non-package vars.
            return(character(0))

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library(ShortRead)
library(parallel)

tsmsg <- function(...) message(format(Sys.time(), "%Y-%m-%d %H:%M:%OS6"), ": ", ...)

## Like readChild but returns NULL when child is finished, and
## automatically unserializes results.
readChildSafe <- function(child) {
    res <- parallel:::readChild(child)
    if (is.integer(res) || is.null(res)) {

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(require 'cl)

(defsubst my-interactive-internal ()
  "Eqivalent of the INTERACTIVE macro in the Emacs C source.

This should never be called directly."
  (and (not executing-kbd-macro) (not noninteractive)))

(defun backtrace-from (fun)
  "Return all backtrace frames, starting with the one for FUN.

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(defun frame-is-last-ns-frame (frame)
  "Returns t if FRAME is the only NS frame."
  (and 
   ;; Frame is ns frame
   (eq (framep frame) 'ns)
   ;; No other frames on same terminal
   (>= 1 (length (filtered-frame-list 
                 (lambda (frm) (eq (frame-terminal frm)
                              (frame-terminal frame))))))))

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--- a/R/gff.R	2012-03-30 15:59:39.000000000 -0700
+++ b/R/gff.R	2012-05-11 17:36:59.208145562 -0700
@@ -286,13 +286,12 @@
                 lines <- rep(seq_along(attrSplit), elementLengths(attrSplit))
                 attrs <- sub(" *$", "", sub("^ *", "", unlist(attrSplit)))
                 if (is(file, "GFF3File")) {
-                  attrs <- paste(attrs, "=", sep = "")
-                  tvSplit <- strsplit(attrs, "=", fixed=TRUE)
-                  if (any(elementLengths(tvSplit) != 2))
+

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import textwrap

def refill_docstring(func, *args, **kwargs):
    """Fix the text wrapping in a function's docstring.

    This can be useful when creating doc strings dynamically.

    Additional args are options to textwrap.TextWrapper."""
    wrapper = textwrap.TextWrapper(*args, **kwargs)
    # Remove trailing whitespace from all lines

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# This file defines a decorator '@log_to()' that logs every call to a
# function, along with the arguments that function was called with. It
# takes a logging function, which is any function that accepts a
# string and does something with it. A good choice is the debug
# function from the logging module. A second decorator '@logdebug' is
# provided that uses 'logging.debug' as the logger.

from __future__ import print_function
from functools import wraps
from inspect import getcallargs, getargspec