jamescasbon

# hmm no imports ;)

class BaseHandler(cyclone.web.RequestHandler):
    def get_current_user(self):
        return self.get_secure_cookie("user")

class LoginHandler(BaseHandler):
    def get(self):
        err = self.get_argument("e", None)
        self.finish("""

jamescasbon

# quickly fix mapping qualities	in samfiles generated by SSAHA2
# mapq 255 is undefined according to spec, but SSAHA2 is not 
# following this convention 
import pysam

infile = pysam.Samfile( "-", "rb" )
outfile = pysam.Samfile( "-", "wb", template = infile )
for s in infile:
    if s.mapq == 255:
        s.mapq = 244

jamescasbon

$ make
cd ../bamtools && mkdir -p build && cd build && cmake .. && make
-- Configuring done
-- Generating done
-- Build files have been written to: /home/james/src/freebayes/bamtools/build
make[1]: Entering directory `/home/james/src/freebayes/bamtools/build'
make[2]: Entering directory `/home/james/src/freebayes/bamtools/build'
make[3]: Entering directory `/home/james/src/freebayes/bamtools/build'
make[3]: Leaving directory `/home/james/src/freebayes/bamtools/build'
make[3]: Entering directory `/home/james/src/freebayes/bamtools/build'

jamescasbon

#!/usr/bin/env python
""" Melt a VCF file into a tab delimited set of calls, one per line

VCF files have all the calls from different samples on one line.  This 
script reads vcf on stdin and writes all calls to stdout in tab delimited 
format with one call in one sample per line.  This makes it easy to find 
a given sample's genotype with, say, grep.
"""

import sys

jamescasbon

"""
A really stupid python template language inspired by coffeekup, markaby.
Do not use this code, it will ruin your day.  A byproduct of insomnia.

TL;DR
-----

This module defines a template language that allows us to do:

    d = Doc()

jamescasbon

d = Doc()
with d.html: 

    with d.head:
        d.title ('example page')
        d.link  (rel='stylesheet', href='/style.css', type='text/css')
    
    with d.body (style='foo'):
        d.a ('other stuff on another page', href='/other.html')

jamescasbon

Feature: Mail
    In order to handle mail

    Scenario: Mail relay
        Given I am a production server
        And I am not a mail server 
        Then I should have postfix installed
        And I should have a mail relay to mail.example.org

    Scenario: Mail server

jamescasbon

from lettuce import *
from fabric import api
from fabric.api import env
import socket


servers = {
        'xxx.local': {
            'ip': ' xxxx',
            'roles': ['production']

jamescasbon

import redis
import inspect

class RedisPlugin(object):
    name = 'redis'

    def __init__(self,host='localhost',port=6379,database=0,keyword='rdb'):
      self.host = host
      self.port = port
      self.database = database

jamescasbon

String file contents