Fixed six_frame_translations function (bug #202606).

(Portage version: 2.1.3.19)

4 files changed, 88 insertions, 2 deletions

diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
index 92407eef7a2e..74a67af5c96a 100644
--- a/sci-biology/biopython/ChangeLog
+++ b/sci-biology/biopython/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/biopython
-# Copyright 2002-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.18 2007/05/17 18:47:30 ribosome Exp $
+# Copyright 2002-2008 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.19 2008/01/30 02:53:58 ribosome Exp $
+
+*biopython-1.44 (30 Jan 2008)
+
+  30 Jan 2008; Olivier Fisette <ribosome@gentoo.org>
+  +files/biopython-1.44-sequtils-complement.patch, +biopython-1.44.ebuild:
+  Fixed six_frame_translations function. Thanks to JTRiley
+  <justin.t.riley@gmail.com> for his patch. (Fixes bug #202606.)
 
 *biopython-1.43 (17 May 2007)
 
diff --git a/sci-biology/biopython/biopython-1.44.ebuild b/sci-biology/biopython/biopython-1.44.ebuild
new file mode 100644
index 000000000000..d60bbfdb1712
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.44.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.44.ebuild,v 1.1 2008/01/30 02:53:58 ribosome Exp $
+
+inherit distutils eutils
+
+DESCRIPTION="Biopython - Python modules for computational molecular biology"
+LICENSE="as-is"
+HOMEPAGE="http://www.biopython.org"
+SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"
+
+SLOT="0"
+IUSE="kdtree"
+KEYWORDS="~alpha ~amd64 ~ppc ~sparc ~x86"
+
+DEPEND=">=dev-lang/python-2.2
+		>=dev-python/egenix-mx-base-2.0.3
+		>=dev-python/numeric-19.0
+		>=dev-python/reportlab-1.11"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}/${PN}-1.43-buildkdtree.patch"
+	epatch "${FILESDIR}/${P}-sequtils-complement.patch"
+	if use kdtree; then
+		sed -i -e 's/USE_KDTREE = False/USE_KDTREE = True/' \
+				setup.py || die "Could not apply patch for KDTree support."
+	fi
+}
+
+src_compile() {
+	distutils_src_compile
+}
+
+src_install() {
+	DOCS="Doc/*.txt Doc/*.tex Doc/install/*.txt"
+	distutils_src_install
+
+	dohtml Doc/install/*.html || die "Failed to install HTML install docs."
+	dohtml Doc/*.html || die "Failed to install HTML docs."
+	cp -r Doc/examples/ Doc/*.pdf ${D}/usr/share/doc/${PF}/ || \
+			die "Failed to install documentation."
+}
diff --git a/sci-biology/biopython/files/biopython-1.44-sequtils-complement.patch b/sci-biology/biopython/files/biopython-1.44-sequtils-complement.patch
new file mode 100644
index 000000000000..16fc44d77cd0
--- /dev/null
+++ b/sci-biology/biopython/files/biopython-1.44-sequtils-complement.patch
@@ -0,0 +1,32 @@
+--- biopython-1.44/Bio/SeqUtils/__init__.py.old	2007-09-14 09:38:35.000000000 -0400
++++ biopython-1.44/Bio/SeqUtils/__init__.py	2007-12-17 11:07:27.000000000 -0500
+@@ -7,8 +7,7 @@
+ # license.  Please see the LICENSE file that should have been included
+ # as part of this package.
+ 
+-import os, sys, getopt, re, time
+-from string import maketrans
++import re, time
+ from Bio import SeqIO
+ from Bio import Translate
+ from Bio.Seq import Seq
+@@ -277,8 +276,9 @@
+    nice looking 6 frame translation with GC content - code from xbbtools
+    similar to DNA Striders six-frame translation
+    """
+-   comp = complement(seq)
+-   anti = reverse(comp)
++   from Bio.Seq import reverse_complement
++   anti = reverse_complement(seq)
++   comp = anti[::-1]
+    length = len(seq)
+    frames = {}
+    for i in range(0,3):
+@@ -399,6 +399,7 @@
+ # {{{ 
+ 
+ if __name__ == '__main__':
++   import sys, getopt
+    # crude command line options to use most functions directly on a FASTA file
+    options = {'apply_on_multi_fasta':0,
+               'quick':0,
diff --git a/sci-biology/biopython/files/digest-biopython-1.44 b/sci-biology/biopython/files/digest-biopython-1.44
new file mode 100644
index 000000000000..d690618f53f6
--- /dev/null
+++ b/sci-biology/biopython/files/digest-biopython-1.44
@@ -0,0 +1,3 @@
+MD5 762c7a358af9dc58b712b8b4bb99d0c2 biopython-1.44.tar.gz 3840036
+RMD160 ecbbe2f46f0e5d124d910632dc9a7fd051202c0b biopython-1.44.tar.gz 3840036
+SHA256 e47c4a7c612e11cb6c1c0515274ce231646b31bbf1c9e3ac58998928c0ad3c72 biopython-1.44.tar.gz 3840036