MurphyMarkW

#!/usr/bin/env python

import string
import argparse

TRANSLATION = string.maketrans('actgACTG', 'tgacTGAC')

def reverse_complement(s):

    return s.translate(TRANSLATION)[::-1]

MurphyMarkW

#!/usr/bin/env python

import os
import sys
import json
import logging
import argparse

import boto
import boto.s3.connection

MurphyMarkW

#!/usr/bin/env python

import json
import logging
import argparse

import boto
import boto.s3.connection

if __name__ == '__main__':

MurphyMarkW

#!/usr/bin/env python

import sys
import json
import mmap
import logging
import argparse

import boto
import boto.s3.connection

MurphyMarkW

#!/usr/bin/env python

import pysam


def is_qc_failed_record(r):
    '''
    For a given pysam.AlignedSegment return True if it is QC failed.
    Otherwise, return False.
    '''

MurphyMarkW

import hmac
import time
import base64
import hashlib

import requests

try: # Python 2.x
    import urlparse as parser
except ImportError: # Python 3.x

MurphyMarkW

#!/usr/bin/env python

import argparse

import pysam


# For standalone execution, add filters here.
# Must take one positional argument.
# Must return True if record is to be rejected.

MurphyMarkW

-- This will eat memory and eventually crash / get killed...
last [1..]

-- While this will spin, but not allocate memory as it goes.
last' [] = error "empty list"
last' [a] = a
last' (a:as) = last' as

MurphyMarkW

#!/usr/bin/env python

import json
import logging

import boto
import boto.s3.connection

if __name__ == '__main__':
    import argparse

MurphyMarkW

#!/usr/bin/env python

import logging

def test(conn, bucket):

    keys = conn.get_bucket(bucket).list()

    for key in keys:
        logging.info('{} {}'.format(bucket, key.name))