4 files changed, 167 insertions, 105 deletions

diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile
index e59a64a4cae6..2787d9a959ea 100644
--- a/biology/py-biopython/Makefile
+++ b/biology/py-biopython/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	biopython
-PORTVERSION=	1.00.a2
+PORTVERSION=	1.00.a3
 CATEGORIES=	biology python
 MASTER_SITES=	http://www.biopython.org/Download/
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -17,16 +17,14 @@ MAINTAINER=	wjv@FreeBSD.org
 
 BUILD_DEPENDS=	${PYDISTUTILS}
 RUN_DEPENDS=	${PYTHON_SITELIBDIR}/Martel/__init__.py:${PORTSDIR}/textproc/py-martel \
-		${PYTHON_SITELIBDIR}/Numeric/Numeric.py:${PORTSDIR}/math/py-numeric
-
-# Biopython requires Python 2.0 or above:
-PYTHON_VERSION=	python2.1
+		${PYTHON_SITELIBDIR}/Numeric/Numeric.py:${PORTSDIR}/math/py-numeric \
+		${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base
 
+USE_PYTHON=	yes
 PLIST_SUB+=	PLIST_CORBA=${PLIST_CORBA} PLIST_OMNIORB=${PLIST_OMNIORB} \
 		PLIST_FNORB=${PLIST_FNORB}
 CPIO=		cpio --quiet -pdum -R
-DOCDIR=		${PREFIX}/share/doc/py-biopython
-EGDIR=		${PREFIX}/share/examples/py-biopython
+EXAMPLESDIR=	${PREFIX}/share/examples/${PORTNAME}
 
 # CORBA support (a.k.a Biopython-CORBA):
 # Set WITH_CORBA to enable CORBA support for the Biopython port.
@@ -41,7 +39,7 @@ EGDIR=		${PREFIX}/share/examples/py-biopython
 # - ORBit is a very popular and elegant ORB.  The ORBit-Python bindings are
 #   used.
 # Since Fnorb is distributed under a non-free licence and ORBit support in
-# Biopython-CORBA is not yet stable, "omniorb" is the default.
+# Biopython-CORBA is reputedly not yet stable, "omniorb" is the default.
 CORBA_ORB?=	omniorb
 
 CORBA_VERSION=	0.2.1
@@ -57,6 +55,7 @@ PLIST_OMNIORB=	""
 PLIST_FNORB=	"@comment "
 .elif ${CORBA_ORB} == "fnorb"
 BUILD_DEPENDS+=	${PYTHON_SITELIBDIR}/Fnorb/__init__.py:${PORTSDIR}/devel/fnorb
+RUN_DEPENDS+=	${PYTHON_SITELIBDIR}/Fnorb/__init__.py:${PORTSDIR}/devel/fnorb
 CORBA_ORBNAME=	Fnorb
 EXTRA_PATCHES+=	${PATCHDIR}/extra-patch-build_helper.py
 PLIST_OMNIORB=	"@comment "
@@ -92,6 +91,9 @@ do-build:
 	@ cd ${CORBA_WRKSRC} && ${PYTHON_CMD} setup.py build
 .endif
 
+pre-install:
+	@ ${SH} ${PKGREQ} INSTALL
+
 do-install:
 	@ cd ${WRKSRC} && ${PYTHON_CMD} setup.py install -c -O1 \
 	  --prefix=${PREFIX}
@@ -102,24 +104,25 @@ do-install:
 
 post-install:
 .if !defined(NOPORTDOCS)
-	@ ${MKDIR} ${DOCDIR}
+	@ ${MKDIR} ${DOCSDIR}
 .for docfiles in *.txt *.tex *.py
-	@ ${INSTALL_DATA} ${WRKSRC}/Doc/${docfiles} ${DOCDIR}
+	@ ${INSTALL_DATA} ${WRKSRC}/Doc/${docfiles} ${DOCSDIR}
 .endfor
-	@ ${MKDIR} ${EGDIR}
-	@ ${INSTALL_DATA} ${WRKSRC}/Doc/examples/*.py ${EGDIR}
+	@ ${MKDIR} ${EXAMPLESDIR}
+	@ ${INSTALL_DATA} ${WRKSRC}/Doc/examples/*.py ${EXAMPLESDIR}
 	@ cd ${WRKSRC} && find Scripts \
-	  | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EGDIR}
+	  | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
 .if defined(WITH_CORBA)
-	@ ${MKDIR} ${DOCDIR}/BioCorba
+	@ ${MKDIR} ${DOCSDIR}/BioCorba
 .for docfiles in *.tex *.pdf
-	@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/${docfiles} ${DOCDIR}/BioCorba
+	@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/${docfiles} ${DOCSDIR}/BioCorba
 .endfor
-	@ ${MKDIR} ${EGDIR}/BioCorba
+	@ ${MKDIR} ${EXAMPLESDIR}/BioCorba
 	@ cd ${CORBA_WRKSRC}/Doc/examples && find * \
-	  | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EGDIR}/BioCorba
-	@ ${MKDIR} ${EGDIR}/BioCorba/Scripts
-	@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Scripts/* ${EGDIR}/BioCorba/Scripts
+	  | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}/BioCorba
+	@ ${MKDIR} ${EXAMPLESDIR}/BioCorba/Scripts
+	@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Scripts/* \
+	  ${EXAMPLESDIR}/BioCorba/Scripts
 .endif	# defined(WITH_CORBA)
 .endif	# !defined(NOPORTDOCS)
 
diff --git a/biology/py-biopython/distinfo b/biology/py-biopython/distinfo
index 5627a525c266..d88599879874 100644
--- a/biology/py-biopython/distinfo
+++ b/biology/py-biopython/distinfo
@@ -1,2 +1,2 @@
-MD5 (biopython-1.00a2.tar.gz) = 416fb1ab08dfdd7f3d4d75bc0043ace8
+MD5 (biopython-1.00a3.tar.gz) = be59a12eeb2c0bcdd82a73dfd7bcc615
 MD5 (biopython-corba-0.2.1.tar.gz) = 3d6d3e4570ff2996bef84e08f6fabc25
diff --git a/biology/py-biopython/pkg-plist b/biology/py-biopython/pkg-plist
index a7b709a312f1..8a4749f0eb0b 100644
--- a/biology/py-biopython/pkg-plist
+++ b/biology/py-biopython/pkg-plist
@@ -201,73 +201,74 @@
 %%PLIST_OMNIORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/ensembl_idl.py
 %%PLIST_OMNIORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/ensembl_idl.pyc
 %%PLIST_OMNIORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/ensembl_idl.pyo
-%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/IntroPythonClient.pdf
-%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/IntroPythonClient.tex
-%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/README.pdf
-%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/README.tex
-%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/biocorbahowto.pdf
-%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/biocorbahowto.tex
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/messenger/__init__.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/messenger__POA/__init__.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/secret_message_client.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/secret_message_idl.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/biosequence_client.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/biosequence_idl.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/servers/__init__.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/servers__POA/__init__.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo/__init__.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo__POA/__init__.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo_client.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo_idl.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/Scripts/bioenv_server.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/a_drought.fasta
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/a_drought.gb
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/embl_biocorba.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/fasta_bioenv.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/fasta_biopy.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/fasta_pseqit.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/fasta_server.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/gb_bioenv.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/gbclient.py
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/gbsrv.pl
-%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/genbank_db_server.py
-%%PORTDOCS%%share/doc/py-biopython/Blast.txt
-%%PORTDOCS%%share/doc/py-biopython/Enzyme.txt
-%%PORTDOCS%%share/doc/py-biopython/Fasta.txt
-%%PORTDOCS%%share/doc/py-biopython/Medline.txt
-%%PORTDOCS%%share/doc/py-biopython/Parser.txt
-%%PORTDOCS%%share/doc/py-biopython/Prosite.txt
-%%PORTDOCS%%share/doc/py-biopython/References.txt
-%%PORTDOCS%%share/doc/py-biopython/SCOP.txt
-%%PORTDOCS%%share/doc/py-biopython/SwissProt.txt
-%%PORTDOCS%%share/doc/py-biopython/Tutorial.tex
-%%PORTDOCS%%share/doc/py-biopython/Tutorial.txt
-%%PORTDOCS%%share/doc/py-biopython/make_api_docs.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/SeqGui/SeqGui.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/query_pubmed.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/README
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/nextorf.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/test.fas
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/testrp.fas
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_blast.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_blastbg.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_io.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_sequence.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_translations.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_utils.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_widget.py
-%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbbtools.py
-%%PORTDOCS%%share/examples/py-biopython/clustal_run.py
-%%PORTDOCS%%share/examples/py-biopython/fasta_consumer.py
-%%PORTDOCS%%share/examples/py-biopython/fasta_dictionary.py
-%%PORTDOCS%%share/examples/py-biopython/fasta_iterator.py
-%%PORTDOCS%%share/examples/py-biopython/getgene.py
-%%PORTDOCS%%share/examples/py-biopython/local_blast.py
-%%PORTDOCS%%share/examples/py-biopython/make_subsmat.py
-%%PORTDOCS%%share/examples/py-biopython/pubmed_search.py
-%%PORTDOCS%%share/examples/py-biopython/query_entrez.py
-%%PORTDOCS%%share/examples/py-biopython/swissprot.py
-%%PORTDOCS%%share/examples/py-biopython/www_blast.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/IntroPythonClient.pdf
+%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/IntroPythonClient.tex
+%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/README.pdf
+%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/README.tex
+%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/biocorbahowto.pdf
+%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/biocorbahowto.tex
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyFirstClient/messenger/__init__.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyFirstClient/messenger__POA/__init__.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyFirstClient/secret_message_client.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyFirstClient/secret_message_idl.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MySecondClient/biosequence_client.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MySecondClient/biosequence_idl.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MySecondClient/servers/__init__.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MySecondClient/servers__POA/__init__.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo/__init__.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo__POA/__init__.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo_client.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo_idl.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/Scripts/bioenv_server.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/a_drought.fasta
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/a_drought.gb
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/embl_biocorba.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/fasta_bioenv.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/fasta_biopy.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/fasta_pseqit.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/fasta_server.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/gb_bioenv.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/gbclient.py
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/gbsrv.pl
+%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/genbank_db_server.py
+%%PORTDOCS%%share/doc/biopython/Blast.txt
+%%PORTDOCS%%share/doc/biopython/Enzyme.txt
+%%PORTDOCS%%share/doc/biopython/Fasta.txt
+%%PORTDOCS%%share/doc/biopython/KEGG.txt
+%%PORTDOCS%%share/doc/biopython/Medline.txt
+%%PORTDOCS%%share/doc/biopython/Parser.txt
+%%PORTDOCS%%share/doc/biopython/Prosite.txt
+%%PORTDOCS%%share/doc/biopython/References.txt
+%%PORTDOCS%%share/doc/biopython/SCOP.txt
+%%PORTDOCS%%share/doc/biopython/SwissProt.txt
+%%PORTDOCS%%share/doc/biopython/Tutorial.tex
+%%PORTDOCS%%share/doc/biopython/Tutorial.txt
+%%PORTDOCS%%share/doc/biopython/make_api_docs.py
+%%PORTDOCS%%share/examples/biopython/Scripts/SeqGui/SeqGui.py
+%%PORTDOCS%%share/examples/biopython/Scripts/query_pubmed.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/README
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/nextorf.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/test.fas
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/testrp.fas
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_blast.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_blastbg.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_io.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_sequence.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_translations.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_utils.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_widget.py
+%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbbtools.py
+%%PORTDOCS%%share/examples/biopython/clustal_run.py
+%%PORTDOCS%%share/examples/biopython/fasta_consumer.py
+%%PORTDOCS%%share/examples/biopython/fasta_dictionary.py
+%%PORTDOCS%%share/examples/biopython/fasta_iterator.py
+%%PORTDOCS%%share/examples/biopython/getgene.py
+%%PORTDOCS%%share/examples/biopython/local_blast.py
+%%PORTDOCS%%share/examples/biopython/make_subsmat.py
+%%PORTDOCS%%share/examples/biopython/pubmed_search.py
+%%PORTDOCS%%share/examples/biopython/query_entrez.py
+%%PORTDOCS%%share/examples/biopython/swissprot.py
+%%PORTDOCS%%share/examples/biopython/www_blast.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/AlignInfo.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/AlignInfo.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/AlignInfo.pyo
@@ -280,6 +281,15 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/Generic.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/__init__.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/__init__.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/fastpairwise.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/fastpairwise.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/fastpairwise.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/pairwise.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/pairwise.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/pairwise.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/support.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/support.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/support.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet/IUPAC.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet/IUPAC.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet/IUPAC.pyo
@@ -358,6 +368,24 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Gobase/__init__.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro/__init__.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro/__init__.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/__init__.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/__init__.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/compound_format.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/compound_format.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/compound_format.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/__init__.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/__init__.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/enzyme_format.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/enzyme_format.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/enzyme_format.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/__init__.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/__init__.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/__init__.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/Record.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/Record.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/Record.pyo
@@ -445,6 +473,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/SProt.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/__init__.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/__init__.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/MaxEntropy.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/MaxEntropy.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/MaxEntropy.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/NaiveBayes.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/NaiveBayes.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/NaiveBayes.pyo
@@ -464,6 +495,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/__init__.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/kMeans.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/kMeans.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/kMeans.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/xkMeans.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/xkMeans.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/xkMeans.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/MultiProc/Scheduler.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/MultiProc/Scheduler.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/MultiProc/Scheduler.pyo
@@ -521,6 +555,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/WWW/__init__.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/__init__.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/__init__.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/__init__.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Bio/sequtils.py
+lib/%%PYTHON_VERSION%%/site-packages/Bio/sequtils.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Bio/sequtils.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.py
 lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo
@@ -540,6 +577,10 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/PDB
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat
+@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme
+@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound
+@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG
+@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Gobase
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/GenBank
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Fasta
@@ -552,24 +593,24 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Align
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/Scripts
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo__POA
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/servers__POA
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/servers
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MySecondClient
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/messenger__POA
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/messenger
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba
-%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/doc/py-biopython/BioCorba
-%%PORTDOCS%%@dirrm share/examples/py-biopython/Scripts/xbbtools
-%%PORTDOCS%%@dirrm share/examples/py-biopython/Scripts/SeqGui
-%%PORTDOCS%%@dirrm share/examples/py-biopython/Scripts
-%%PORTDOCS%%@dirrm share/examples/py-biopython
-%%PORTDOCS%%@dirrm share/doc/py-biopython
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/Scripts
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo__POA
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyThirdClient
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MySecondClient/servers__POA
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MySecondClient/servers
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MySecondClient
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyFirstClient/messenger__POA
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyFirstClient/messenger
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyFirstClient
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba
+%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/doc/biopython/BioCorba
+%%PORTDOCS%%@dirrm share/examples/biopython/Scripts/xbbtools
+%%PORTDOCS%%@dirrm share/examples/biopython/Scripts/SeqGui
+%%PORTDOCS%%@dirrm share/examples/biopython/Scripts
+%%PORTDOCS%%@dirrm share/examples/biopython
+%%PORTDOCS%%@dirrm share/doc/biopython
 %%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org_skel/ensembl_skel
 %%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org_skel/biocorba_skel/seqcore_skel
 %%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org_skel/biocorba_skel
@@ -597,3 +638,4 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo
 %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio
 %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters
 %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba
+
diff --git a/biology/py-biopython/pkg-req b/biology/py-biopython/pkg-req
new file mode 100644
index 000000000000..481af4e9a7ad
--- /dev/null
+++ b/biology/py-biopython/pkg-req
@@ -0,0 +1,17 @@
+#!/bin/sh
+
+PATH=$PATH:/usr/local/bin
+
+if [ "x$1" = "xINSTALL" -o "x$2" = "xINSTALL" ]; then
+  PYTHON_GT=`python -c 'import string, sys; \
+                        print string.split(sys.version)[0] >= "2.0"'`
+  if [ "x${PYTHON_GT}" = "x1" ]; then
+    exit 0
+  else
+    echo "-----------------------------------------------------------"
+    echo "Biopython requires Python version 2.0 or greater -         "
+    echo "  please update your Python installation before proceeding."
+    echo "-----------------------------------------------------------"
+    exit 1
+  fi
+fi