brendano

# Written by Brendan O'Connor, brenocon@gmail.com, www.anyall.org
#  * Originally written Aug. 2005
#  * Posted to gist.github.com/16173 on Oct. 2008

#   Copyright (c) 2003-2006 Open Source Applications Foundation
#
#   Licensed under the Apache License, Version 2.0 (the "License");
#   you may not use this file except in compliance with the License.
#   You may obtain a copy of the License at
#

munhitsu

# In case you had some strange python installation
# NOTE: .pydistutils.cfg seems to be not compatible with brew install python
# areas I needed to clean before installation
# clean up ~/Library/Python
# clean up .local

# preconditions:
# xcode with command line tools installed
xcode-select --install

pithyless

Install Python

$ brew install readline sqlite gdbm
$ brew install python --universal --framework
$ python --version
Python 2.7

Symlinks...

daltonmatos

import mock

class AlmostAlwaysTrue(object):

    def __init__(self, total_iterations=1):
        self.total_iterations = total_iterations
        self.current_iteration = 0

    def __nonzero__(self):
        if self.current_iteration < self.total_iterations:

cgoldberg

#!/usr/bin/env python

"""MailBox class for processing IMAP email.

(To use with Gmail: enable IMAP access in your Google account settings)

usage with GMail:

    import mailbox

temoto

def namedlist(typename, field_names):
    """Returns a new subclass of list with named fields.

    >>> Point = namedlist('Point', ('x', 'y'))
    >>> Point.__doc__                   # docstring for the new class
    'Point(x, y)'
    >>> p = Point(11, y=22)             # instantiate with positional args or keywords
    >>> p[0] + p[1]                     # indexable like a plain list
    33
    >>> x, y = p                        # unpack like a regular list

chintak

# First install homebrew
ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"

# Choose the name of the virtualenv as simplecv
virtualenv simplecv --no-site-packages
source simplecv/bin/activate
# This activates the virtualenv; your command prompt should change from `$` to `(simplecv)$`

# Next the dependencies
sudo easy_install pip  # Can be ignored, if pip already present

debugger87

import org.apache.spark.sql.catalyst.expressions.Row
import org.apache.spark.sql.catalyst.types._

import scala.collection.mutable.{ArrayBuffer}

object SparkRowFormatter {

  def formatRowsWithSchema(rowArr: Array[Row], schema: StructType) = {
    rowArr.map(r => formatStruct(schema.fields, r))
  }

msukmanowsky

from pyspark import SparkContext


def main():
    sc = SparkContext(appName="Test Compression")
    # RDD has to be key, value pairs
    data = sc.parallelize([
        ("key1", "value1"),
        ("key2", "value2"),
        ("key3", "value3"),

nikhilRP

import org.bdgenomics.formats.avro.AlignmentRecord
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.projections.Projection
import org.apache.spark.rdd.RDD
import org.apache.parquet.filter2.dsl.Dsl._
import org.apache.parquet.filter2.predicate.FilterPredicate
import org.bdgenomics.adam.projections.AlignmentRecordField._
 
val adamFile = "/user/nikhilrp/encoded-data/mm10/chr1/ENCFF891NNX.adam"
val proj = Projection(readName, contig, start, end, qual)