cldotdev

function showLineNumbers() {
 /************************************ 
 * Written by Andreas Papadopoulos   *
 * http://akomaenablog.blogspot.com  *
 * akoma1blog@yahoo.com              *
 ************************************/
  var isIE = navigator.appName.indexOf('Microsoft') != -1;

  var preElems = document.getElementsByTagName('pre');
  if (preElems.length == 0) return;

cldotdev

###########################################################################################
## Compute N50 values for Assembly Results and Plot their Cumulative Length Distribution ##
###########################################################################################
## Author: Thomas Girke
## Last update: January 28, 2010
## Utilities: Compute N50 and plot cumulative length distribution.
## More details can be found here: http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Analyzing-Assembly-Results

## Overview:
## The N50 is a weighted median statistic such that 50% of the entire assembly 

cldotdev

# Copy these snippets to /etc/fstab
tmpfs   /tmp       tmpfs   defaults,noatime,mode=1777   0  0
tmpfs   /var/spool tmpfs   defaults,noatime,mode=1777   0  0
tmpfs   /var/tmp   tmpfs   defaults,noatime,mode=1777   0  0
tmpfs   /var/log   tmpfs   defaults,noatime,mode=0755   0  0
tmpfs   /home/XXX/.cache   tmpfs   defaults,noatime,mode=0775,uid=YYY,gid=ZZZ   0  0
# XXX = user name
# Get YYY and ZZZ (eg. uid=1000, gid=1000) by typing the command:
# $ id [user name]
# in your bash shell

cldotdev

# http://openwetware.org/wiki/Wilke:ParseDSSP


import re

class DSSPData:
  def __init__(self):
      self.num    = []
      self.resnum = []
      self.moltyp = []

cldotdev

#!/usr/bin/env python3
#
# fixname - Fix hit name in the blastlist
#
# Copyright (C) 2013, Jian-Long Huang
# Licensed under The MIT License
# http://opensource.org/licenses/MIT
#
# Author: Jian-Long Huang (jianlong@ntu.edu.tw)
# Version: 0.1

cldotdev

#!/usr/bin/env python
# http://marlonyao.iteye.com/blog/905313
# Usage: $ python sandbox.py <untrusted.py>

_builtins = dict(__builtins__.__dict__)


def _hook_import(name, *args, **kwargs):
    restricted_modules = [
        'os',

cldotdev

# http://stackoverflow.com/questions/1175208/elegant-python-function-to-convert-camelcase-to-camel-case

def convert(name):
    s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name)
    return re.sub('([a-z0-9])([A-Z])', r'\1_\2', s1).lower()

cldotdev

# This is a standard python config file
# Valid values can be True, False, integer numbers, strings
# By default bpython will look for ~/.config/bpython/config or you
# can specify a file with the --config option on the command line

# General section tag
[general]

# Display the autocomplete list as you type (default: True).
# When this is off, you can hit tab to see the suggestions.

cldotdev

vardef FUNCTION = '[[:blank:]]([[:alpha:]]|_)[[:word:]]*(?=[[:blank:]]*\()'
function = $FUNCTION

keyword = "and|assert|break|class|continue|def|del|elif|else|except|exec",
          "finally|for|global|if|in|is|lambda|not|or|pass",
          "print|raise|return|try|while|self"

cldotdev

# http://stackoverflow.com/questions/2831212/python-sets-vs-lists

>>> import timeit
>>> a = set(range(1000000))
>>> b = range(1000000)
>>> def test_a():
...     '9999' in a
... 
>>> def test_b():
...     '9999' in b