jeetsukumaran

#! /usr/bin/env python


import dendropy
from dendropy.calculate import popgenstat

d = dendropy.DnaCharacterMatrix.get_from_path(
        "data/primates.chars.nexus", "nexus")
print("num_segregating_sites = {}".format(popgenstat.num_segregating_sites(d, True)))
print("num_segregating_sites = {}".format(popgenstat.num_segregating_sites(d, False)))

jeetsukumaran

" Notes:
"   (1) To enhance the ergonomics of this sufficiently to make it practical, at
"       least, until your brain grows a new lobe dedicated to counting line offsets
"       in the background while you work, you should either make sure you have
"       something like the following in your `~/.vimrc`:
"
"           set number
"           if has('autocmd')
"           augroup vimrc_linenumbering
"               autocmd!

jeetsukumaran

#! /usr/bin/env python

"""
Python Golf

An expression that takes predicate function object and an iterable,
and returns True if the predicate function evaluates True once and exactly once
when applied to all the elements in the iterable.

Expression with the minimum number of non-whitespace characters wins.

jeetsukumaran

function! s:_setup_cidictcompletion()
    let g:_old_ignorecase_state=&ignorecase
    inoremap <C-X><C-K> <ESC>:let g:_old_ignorecase_state=&ignorecase<CR>:set ignorecase<CR>:set infercase<CR>a<C-X><C-K>
    " inoremap <expr> <CR> pumvisible() ? "\<C-y><ESC>:set noignorecase<CR>a" : "\<C-g>u\<CR>"
    " inoremap <expr> <C-J> pumvisible() ? "\<C-y><ESC>:set noignorecase<CR>a" : "\<C-g>u\<C-J>"
    let restore=' pumvisible() ? "\<C-y><ESC>:let &ignorecase=g:_old_ignorecase_state<CR>'
    for key in ["<CR>", "<C-J>", "<C-Y>"]
        execute "inoremap <expr> " . key . restore . 'a" : "\<C-g>u\<CR>"'
    endfor
    for key in ["<ESC>", "<C-C>"]

jeetsukumaran

#! /bin/bash

cd venvs

virtualenv -p /opt/python/Python-2.7.6/bin/python2 dendropy4-python2.7 && cd ../dendropy && . ../venvs/dendropy4-python2.7/bin/activate && python setup.py develop && deactivate && cd -
virtualenv -p /opt/python/Python-3.2.5/bin/python3 dendropy4-python3.2 && cd ../dendropy && . ../venvs/dendropy4-python3.2/bin/activate && python setup.py develop && deactivate && cd -
virtualenv -p /opt/python/Python-3.3.4/bin/python3 dendropy4-python3.3 && cd ../dendropy && . ../venvs/dendropy4-python3.3/bin/activate && python setup.py develop && deactivate && cd -
virtualenv -p /opt/python/Python-3.4.0/bin/python3 dendropy4-python3.4 && cd ../dendropy && . ../venvs/dendropy4-python3.4/bin/activate && python setup.py develop && deactivate && cd -

virtualenv -p /opt/python/Python-2.6.9/bin/python2 dendropy3-python2.6 && cd ../dendropy3 && . ../venvs/dendropy4-python2.6/bin/activate && python setup.py develop && deactivate && cd -

jeetsukumaran

"""A caseless dictionary implementation."""

from collections import MutableMapping


class CaselessDictionary(MutableMapping):

    """
    A dictionary-like object which ignores but preserves the case of strings.

jeetsukumaran

#! /usr/bin/env python

__version__ = "1.0.0"

from time import strftime
import random
import sys
import os
import argparse

jeetsukumaran

#! /usr/bin/env python

import subprocess
import optparse
import os
import sys

__version__ = "1.0.0"
__author__ = "Jeet Sukumaran"

jeetsukumaran

on run
  do shell script "/Applications/MacVim.app/Contents/MacOS/Vim -g > /dev/null 2>&1"
end run

jeetsukumaran

# INSTRUCTIONS: save as ~/.gdbinit
# REVISION : 6.1 
# CONTRIBUTORS: mammon_, elaine, pusillus, mong
# NOTES: 'help user' in gdb will list the commands/descriptions in this file
#        'context on' now enables auto-display of context screen
#
# CHANGELOG:
#  Version 6.1
#        fixed filename in step_to_call so it points to /dev/null
#        changed location of logfiles from /tmp  to ~