jeetsukumaran

#! /usr/bin/env python

__version__ = "1.0.0"

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

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

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

#! /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

#! /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

Phylogenetic Analysis: Multi-Processor RAxML Partitioned Maximum Likelihood Under SGE

Model File (model.txt)

DNA, cr = 1-732

jeetsukumaran

Phylogenetic Analysis: Parallel Mr. Bayes on a Cluster under SGE

Mr. Bayes Block

begin mrbayes;

jeetsukumaran

Phylogenetic Analysis: Single-Processor RAxML Partitioned Maximum Likelihood

Model File (model.txt)

DNA, cr = 1-732

jeetsukumaran

Phylogenetic Analysis: Multi-Processor RAxML Non-Parametric Bootstraps Under SGE

Model File (model.txt)

DNA, cr = 1-732

jeetsukumaran

# Phylogenetic Analysis: Parallel Mr. Bayes on a Cluster under Torque (PBS) and OpenMP
# Selects 3 machines, and 4 cpu's on each machine
#PBS -N mrbayes
#PBS -W group_list="max_ittc"
#PBS -q max_ittc
#PBS -l nodes=3:ncpus=4
cd $PBS_O_WORKDIR
mpirun -np 12 /share/apps/bin/mb-multi-cvs-3.2 pythonidae.mb