garrettr

def upload_to_s3(local_file, bucket_name, key_name=None, acl='private'):
    '''
    Uploads local_file to bucket_name on Amazon S3

    key_name is the "filename" on Amazon S3. We'll default to the local file's name if
    no alternative key_name is specified.
    '''
    # connect to Amazon S3
    conn = S3Connection(AWS_ACCESS_KEY, AWS_SECRET_KEY)
    bucket = conn.create_bucket(bucket_name)

garrettr

from django.core.management.base import BaseCommand, CommandError
from news.models import Post

from django.core.files import File
from django.conf import settings
from feincms.module.medialibrary.models import MediaFile

import sys, os
import imaplib
import email

garrettr

CC=clang
CFLAGS=-O3 -msse2 -Wall -Wextra -D_FILE_OFFSET_BITS=64
objects := $(patsubst %.c,%.o,$(wildcard *.c))

all: statmap statmap.so
statmap: $(objects)
	$(CC) -o statmap \
	$(objects) \
	$(CFLAGS) \
	-lm -lpthread

garrettr

# Bold green prompt
# ~ > 
export PS1="\[\e[1;32m\]\W > \[\e[m\]"

# Officially the coolest prompt ever (inverted black-on-green \W)
export PS1="\[\e[7;32m\]\W \$\[\e[m\] "

# for more: http://jamiedubs.com/ps1-collection-customize-your-bash-prompt/

garrettr

# Plan for finishing Gapped Reads Mapping

Here is the remaining work that needs to be done to map gapped reads (RNASeq) with Statmap.

1. [x] Change the binary search in find_matching_mapped_locations to return as matches all locations within a range (REFERENCE_INSERT_LENGTH_MAX in config.h) including and beyond the base location's start.
Done on: 8/31/12
2. [x] Handle multiple matches in the candidate mapping building. Storing them is easy (we used a mapped_locations from the beginning with this in mind).
Done on: 9/3/12

Once that is done, we will have a set of candidate mappings, as we had before. The next step is to rework the recheck. As preparation, the first step is

garrettr

from flask import Flask
from flask.ext.sqlalchemy import SQLAlchemy

app = Flask(__name__)
app.config.from_pyfile('settings.cfg')
db = SQLAlchemy(app)

class User(db.Model):
    __tablename__ = 'users'
    

garrettr

In [1]: from __future__ import division

In [2]: n = 2**32

In [3]: p = 1 - ((n-1)/n)**1000000000

In [4]: p
Out[4]: 0.2077122589016286

garrettr

#!/usr/bin/env python

import sys

wordlist_filename = sys.argv[1]

words = []
with open(wordlist_filename) as wl_fp:
	for line in wl_fp:
		words.append(line.strip())

garrettr

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

I, Garrett Robinson, downloaded the Qubes signing key on

Sun Apr  6 16:11:37 PDT 2014

from

https://keys.qubes-os.org/keys/qubes-developers-keys.asc

garrettr

diff --git a/lib/userStorage.js b/lib/userStorage.js
index 5441382..5cca0cc 100644
--- a/lib/userStorage.js
+++ b/lib/userStorage.js
@@ -104,6 +104,10 @@ exports.init = function()
       if (!storage[store]) storage[store] = {};
     }
   );
+  // Log JSON out to the console for cooperq
+  userStored.forEach(function(store) {