jeetsukumaran

#! /bin/bash

if [[ -z $1 ]]
then
    if [[ -z $VIMRUNTIME ]]
    then
        VIMRUNTIME=$HOME/.vim
    fi
else
    VIMRUNTIME="$1"

jeetsukumaran

#! /usr/bin/env python

###############################################################################
##
##  Copyright 2011 Jeet Sukumaran.
##
##  This program is free software; you can redistribute it and/or modify
##  it under the terms of the GNU General Public License as published by
##  the Free Software Foundation; either version 3 of the License, or
##  (at your option) any later version.

jeetsukumaran

#! /usr/bin/env python

from dendropy.interop import ncbi

entrez = ncbi.Entrez(generate_labels=True,
            label_num_desc_components=2,
            label_separator='_',
            exclude_gbnum_from_label=True,
            sort_taxa_by_label=True)

jeetsukumaran

#! /usr/bin/env python

import os
import sys
import dendropy

src_filepath = sys.argv[1]
full_data = dendropy.DnaCharacterMatrix.get_from_path(src_filepath, 'nexus')
items = full_data.character_subsets.items()
basename = os.path.splitext(os.path.basename(src_filepath))[0]

jeetsukumaran

#! /bin/bash

compose_name() {
    if [[ $(which git 2> /dev/null) ]]
    then
        STATUS=$(git status 2>/dev/null)
        if [[ -z $STATUS ]]
        then
            return
        fi

jeetsukumaran

#! /bin/bash

if [[ -z $1 ]]
then
    echo "require version number (e.g. "2.2.4") as argument"
    exit
fi
VERSION="$1"
NOW=$(date +"%Y%b%d")
SRC="satesrc-v$VERSION-$NOW"

jeetsukumaran

#! /bin/bash

function usage {
    echo "`basename $0` [OPTIONS] [OUTPUT-PREFIX]"
    echo "Archives Vim installation."
    echo " "
    echo "Options:"
    echo "  --windows           ... build distributable for MS Windows system"
    echo "  -h|--help           ... show help"
    exit 1

jeetsukumaran

#############################################################################
# Original code ported from the Java reference code by Bram Cohen, April 2001,
# with the following statement:
#
#         this code is public domain, unless someone makes
#         an intellectual property claim against the reference
#         code, in which case it can be made public domain by
#         deleting all the comments and renaming all the variables
#
class Rijndael(object):

jeetsukumaran

#! /usr/bin/env python
 
###############################################################################
##
##  Copyright 2012 Jeet Sukumaran.
##
##  This program is free software; you can redistribute it and/or modify
##  it under the terms of the GNU General Public License as published by
##  the Free Software Foundation; either version 3 of the License, or
##  (at your option) any later version.

jeetsukumaran

#! /usr/bin/env python

##############################################################################
# Following functions have been taken from the DendroPy library from:
##
##  DendroPy Phylogenetic Computing Library.
##
##  Copyright 2010 Jeet Sukumaran and Mark T. Holder.
##  All rights reserved.
##