brantfaircloth

"""
File: check_sum.py
Author: Brant Faircloth

Created by Brant Faircloth on 23 February 2012 10:02 PST (-0800)
Copyright (c) 2012 Brant C. Faircloth. All rights reserved.

Description: Check a list of files against hashes.

License:  http://www.opensource.org/licenses/BSD-3-Clause

brantfaircloth

Cheaper, smaller

Add in SSD or two for fast IO ops. 4 internal HDD slots.

Part	p/n	cost	units	total cost	comment
CPU	BX80614E5645	$557.00	2	$1,114.00	12 cores @ 2.4 GHZ

brantfaircloth

class FullPaths(argparse.Action):
    """Expand user- and relative-paths"""
    def __call__(self, parser, namespace, values, option_string=None):
        setattr(namespace, self.dest, os.path.abspath(os.path.expanduser(values)))

def is_dir(dirname):
    """Checks if a path is an actual directory"""
    if not os.path.isdir(dirname):
        msg = "{0} is not a directory".format(dirname)
        raise argparse.ArgumentTypeError(msg)

brantfaircloth

"""
File: refgene_to_bed.py
Author: Brant Faircloth

Created by Brant Faircloth on 06 December 2011 22:12 PST (-0800)
Copyright (c) 2011 Brant C. Faircloth. All rights reserved.

Description: convert UCSC refgene.txt files to BED format 

"""

brantfaircloth

cp /System/Library/Extensions/IOAHCIFamily.kext/Contents/PlugIns/IOAHCIBlockStorage.kext/Contents/MacOS/IOAHCIBlockStorage ~/Desktop/IOAHCIBlockStorage.original
sudo perl -pi -e 's|(\x52\x6F\x74\x61\x74\x69\x6F\x6E\x61\x6C\x00).{9}(\x00\x51)|$1\x00\x00\x00\x00\x00\x00\x00\x00\x00$2|sg' /System/Library/Extensions/IOAHCIFamily.kext/Contents/PlugIns/IOAHCIBlockStorage.kext/Contents/MacOS/IOAHCIBlockStorage

sudo kextcache -system-prelinked-kernel
sudo kextcache -system-caches

brantfaircloth

class Writer(writers.Writer):
         setting_spec = (
             ('Specify the maximum width (in characters) for options in option '
              'lists.  Longer options will span an entire row of the table used '
              'to render the option list.  Default is 14 characters.  '
              'Use 0 for "no limit".',
              ['--option-limit'],
              {'default': 4, 'metavar': '<level>',
              'validator': frontend.validate_nonnegative_int})
         )

brantfaircloth

import time
import random
from multiprocessing import Process, Queue, JoinableQueue, cpu_count

""" Adjust time.sleep() values to see action of consumer """

def work(id, jobs, result):
    while True:
        task = jobs.get()
        if task is None:

brantfaircloth

class FullPaths(argparse.Action):
    """Expand user- and relative-paths"""
    def __call__(self, parser, namespace, values, option_string=None):
        setattr(namespace, self.dest, os.path.abspath(os.path.expanduser(values)))

def get_args():
    parser = argparse.ArgumentParser(description='Something smart here')
    parser.add_argument('my_conf', help='The configuration file for the db', action = FullPaths)
    return parser.parse_args()

brantfaircloth

• get hyphy source (http://www.datam0nk3y.org/)

• get sqlite source (http://www.sqlite.org/download.html) - you want the "amalgamation"

• unzip hyphy source somewhere

• unzip sqlite source somewhere

• remove the shell.c file from the sqlite source

• edit buildFromSVN.sh to point to your svn files:

    cp /path/to/sqlite-amalgamation-*/*.{c,h} $installDirectory/Source/SQLite/
  

• run bash buildFromSVN.sh

brantfaircloth

# get singleton reads names from assembly stats:

grep Singleton 454ReadStatus.txt > singles.txt

# if you assembled using fasta+qual files, use faSomeRecords from kent source:

faSomeRecords ../reads/schisto.454reads.combined.fsa singles.txt singles.fa

# if you assembled using SFF files: