# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$

EAPI=5

PYTHON_COMPAT=( python2_7 )

inherit distutils-r1

DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences"
HOMEPAGE="https://github.com/ged-lab/khmer"
SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"

LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""

DEPEND=""
RDEPEND="sci-biology/screed"

python_prepare_all(){
	rm -rf lib/{bzip2,zlib} || die

	sed \
		-e 's:zlib/zlib.h:zlib.h:g' \
		-e 's:bzip2/bzlib.h:bzlib.h:g' \
		-i lib/read_parsers.hh lib/counting.cc || die

	sed \
		-e "/extra_objects/d" \
		-e "s:'nose >= 1.0', ::g" \
		-e "s:'sphinx',::g" \
		-e '/libraries/s:, ]:, "z", "bz2", ]:g' \
		-e "s:'-O3',::g" \
		-i setup.py || die

	distutils-r1_python_prepare_all
}