indraniel

package main

import (
	"fmt"
	"log"
	"os"
	"os/signal"
	"strings"
	"syscall"

indraniel

package main

import (
	"fmt"
	"log"
	"math"
	"os"
	"os/signal"
	"strconv"
	"strings"

indraniel

package main

import (
	"fmt"
	"log"
	"math"
	"os"
	"os/signal"
	"strconv"
	"strings"

indraniel

#!/usr/bin/python

from __future__ import print_function

# from https://wiki.python.org/moin/SortingListsOfDictionaries
def multikeysort(items, columns):
    from operator import itemgetter
    comparers = [ ((itemgetter(col[1:].strip()), -1) if col.startswith('-') else (itemgetter(col.strip()), 1)) for col in columns]
    def comparer(left, right):
        for fn, mult in comparers:

indraniel

#!/usr/bin/env Rscript

args <- commandArgs(trailingOnly=TRUE)
file <- args[1]
cat(paste("Processing: ", file, "\n"))

library(knitr)
knit(file)

indraniel

A useful starter skeleton layout for analytics project.

project-dir 
├── README.md
├── bin
├── data
│   ├── derived
│   ├── original
│   └── test

├── docs

indraniel

#!/usr/bin/awk -f

# taken from: http://stackoverflow.com/questions/1729824/transpose-a-file-in-bash
{
    for (i=1; i<=NF; i++)  {
        a[NR,i] = $i
    }
}
NF>p { p = NF }
END {

indraniel

#!/usr/bin/env python

# This is a script to merge multiple [GATK][0] Report (or [GATKReport][1])
# files into a single report file.  This is useful when one is running multiple
# GATK commands on a partitioned [VCF][2] data set for performance reasons, and then
# afterwards assembling up the overall output.
#
# Currently this script supports the GATKReports for the following
# [VariantEval][3] Evaluation Module [outputs][4]:
#

indraniel

#!/usr/bin/env python

from __future__ import print_function, division
import sys, os, pprint
from glob import glob

import requests
from lxml import html
from toolz.curried import *

indraniel

.PHONY: clean

PRJDIR := /path/to/project
DOCS := $(PRJDIR)/docs
RLIBS := /gscmnt/gc2801/analytics/idas/jira/BIO-1465/rpkgs
REPORTDIR := $(DOCS)/writeups
PDFLATEX := /home/archive/texlive-2015/2015/bin/x86_64-linux/pdflatex

writeup: $(REPORTDIR)/report.pdf