Fixed six_frame_translations function (bug #202606).

Package-Manager: portage-2.1.3.19

5 files changed, 104 insertions, 6 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/Manifest b/sci-biology/biopython/Manifest
index e6a84c16f7b2..4ef31d2613a9 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -2,8 +2,13 @@ AUX biopython-1.43-buildkdtree.patch 981 RMD160 3930f852a6ed3b783390d00e7c3ffdec
 MD5 466cc7a8ff9800e06801708e223db549 files/biopython-1.43-buildkdtree.patch 981
 RMD160 3930f852a6ed3b783390d00e7c3ffdeccd2ee270 files/biopython-1.43-buildkdtree.patch 981
 SHA256 6cbce6137e90670a53f83c4ac6c9c83523aa4b7730ed691a8be6fd884a4ddb9e files/biopython-1.43-buildkdtree.patch 981
+AUX biopython-1.44-sequtils-complement.patch 1033 RMD160 d7f8822ad8946e364bb4491a502055e7bf482478 SHA1 f08b0659db5053f13a7f871f037d5beb133745c8 SHA256 9e2f0e85e8be14971667037ac49edec94d73241c88a7cf9caeba6234955ed780
+MD5 bab2613dd83d763460ca816118f91c62 files/biopython-1.44-sequtils-complement.patch 1033
+RMD160 d7f8822ad8946e364bb4491a502055e7bf482478 files/biopython-1.44-sequtils-complement.patch 1033
+SHA256 9e2f0e85e8be14971667037ac49edec94d73241c88a7cf9caeba6234955ed780 files/biopython-1.44-sequtils-complement.patch 1033
 DIST biopython-1.42.tar.gz 3933507 RMD160 9f3027fb1b3326885376eaf7a5a714a26e0bc333 SHA1 107321d782b0a00bc3c302cd8c7e4b82c013d6d7 SHA256 ba4d00fdf7de67196ecba317dee09a14850b40596bd83d73e458c5f19fc9fc58
 DIST biopython-1.43.tar.gz 3867907 RMD160 d7d326659032f9587b85b339941ecb306b694403 SHA1 030e60be1686c81a289dde72811642636a094a28 SHA256 eb424da9efddbf376c31660786ecb34ff893ea752bf7300f4a06d1b8c6ba175b
+DIST biopython-1.44.tar.gz 3840036 RMD160 ecbbe2f46f0e5d124d910632dc9a7fd051202c0b SHA1 ca2a35c9e92a219256fe4fc2a232df5328f9f5d9 SHA256 e47c4a7c612e11cb6c1c0515274ce231646b31bbf1c9e3ac58998928c0ad3c72
 EBUILD biopython-1.42.ebuild 843 RMD160 b5894c9b6cd76e24e0968829908bc71ad064dd0b SHA1 80c6e3f57a2644ab83015cb1fd4e2744cff39003 SHA256 003a04d3d6f6fcfacae68a828726f52020d2c7f32f493813e928deff4d4f2538
 MD5 4f5b0b5715dd800f0b777304738fcf5f biopython-1.42.ebuild 843
 RMD160 b5894c9b6cd76e24e0968829908bc71ad064dd0b biopython-1.42.ebuild 843
@@ -12,10 +17,14 @@ EBUILD biopython-1.43.ebuild 1224 RMD160 fda3e428e88912202ecd8f938d51b6d6c7e22c8
 MD5 1784c8af162b65ce450abf73cd0dc904 biopython-1.43.ebuild 1224
 RMD160 fda3e428e88912202ecd8f938d51b6d6c7e22c80 biopython-1.43.ebuild 1224
 SHA256 1a127fc3189f323b4349ec32e78130dec22a4731a507fbdf1edf14ceebe29647 biopython-1.43.ebuild 1224
-MISC ChangeLog 4141 RMD160 3852e23f777d2d09c9745e455283b645b06a67f5 SHA1 b4d160607e4d97837522b5b206a1d37681b15920 SHA256 4ae1bfe339f800e93f3c768738770de09891e16779912288a782f2ab51c6bb99
-MD5 3f96352617fbbb3ce75893af1a6e85a6 ChangeLog 4141
-RMD160 3852e23f777d2d09c9745e455283b645b06a67f5 ChangeLog 4141
-SHA256 4ae1bfe339f800e93f3c768738770de09891e16779912288a782f2ab51c6bb99 ChangeLog 4141
+EBUILD biopython-1.44.ebuild 1283 RMD160 9b92d5b876aa4461d14d156fd35408a9661c6b04 SHA1 805e7277ef00ee27e123c3af588a9dbd969cc270 SHA256 095ba6142a0830f8e7ceb7350ca60149b27152b873bbd2b472d324a67febb322
+MD5 a01d7c847f01db81d2a22c4f523edaf1 biopython-1.44.ebuild 1283
+RMD160 9b92d5b876aa4461d14d156fd35408a9661c6b04 biopython-1.44.ebuild 1283
+SHA256 095ba6142a0830f8e7ceb7350ca60149b27152b873bbd2b472d324a67febb322 biopython-1.44.ebuild 1283
+MISC ChangeLog 4425 RMD160 c416e189705e9025fec10c6685528b3d82e4849a SHA1 0df876531a2d8198fe554e137bc408fa1b29b1e0 SHA256 4784d6e8ab63e52910ebbca82c297e327927f06cf7a5572b51f94eecc24b1a6e
+MD5 2fd4eb696ae4744bcdf3a6315b945c39 ChangeLog 4425
+RMD160 c416e189705e9025fec10c6685528b3d82e4849a ChangeLog 4425
+SHA256 4784d6e8ab63e52910ebbca82c297e327927f06cf7a5572b51f94eecc24b1a6e ChangeLog 4425
 MISC metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 SHA1 3c024ca60a2b93ed0e0311f6b05ef5ef117bee31 SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f
 MD5 5f35ae4b4cb1cd144db7c7c093d3fd80 metadata.xml 262
 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 metadata.xml 262
@@ -26,3 +35,6 @@ SHA256 ecaf906566a4d758f5ac3f8ffeecca195eae920c614579c2d64ecb307ce2c7dc files/di
 MD5 21edeaf080b13692cd78336c1b0a69be files/digest-biopython-1.43 247
 RMD160 5d54095533d604b5c8be8e504d1130b31bac5d97 files/digest-biopython-1.43 247
 SHA256 c0e41064db41cdbd073b3aeb2bb2a1daaf8a333bf197aad6e075a94b04d1e1b7 files/digest-biopython-1.43 247
+MD5 a4b7eabdc2b67382d8160a94a0a1309a files/digest-biopython-1.44 247
+RMD160 a4356748c264f6cd623666ec8118134616cdccca files/digest-biopython-1.44 247
+SHA256 1bc8178234a3d25bae300b4be2516278865b99d3e3354cd4825bbb02c9f7ea24 files/digest-biopython-1.44 247
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