- Update to 138038

PR:		138038
Submitted by:	Wen Heping <wenheping@gmail.com>
Approved by:	maintainer

4 files changed, 152 insertions, 444 deletions

diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile
index 2453ff42d728..da21f24b015a 100644
--- a/biology/py-biopython/Makefile
+++ b/biology/py-biopython/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	biopython
-PORTVERSION=	1.48
+PORTVERSION=	1.51
 CATEGORIES=	biology python
 MASTER_SITES=	http://www.biopython.org/DIST/
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -14,13 +14,11 @@ PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 MAINTAINER=	mauricio@arareko.net
 COMMENT=	A collection of Python modules for bioinformatics
 
-BUILD_DEPENDS=	${PYNUMERIC} \
+BUILD_DEPENDS=	${PYNUMPY} \
 		${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base
 RUN_DEPENDS=	${BUILD_DEPENDS}
 
-CONFLICTS=	py*-martel-[0-9]*
-
-USE_PYTHON=	2.3+
+USE_PYTHON=	2.4+
 USE_PYDISTUTILS=yes
 
 .if !defined(WITHOUT_REPORTLAB)
diff --git a/biology/py-biopython/distinfo b/biology/py-biopython/distinfo
index 6b608d2696dd..e8ed6b63e536 100644
--- a/biology/py-biopython/distinfo
+++ b/biology/py-biopython/distinfo
@@ -1,3 +1,3 @@
-MD5 (biopython-1.48.tar.gz) = b049e3af8128bea68e4e86b55c6d0996
-SHA256 (biopython-1.48.tar.gz) = cfb3a1774d1d4b01a66b3428cec7b4c943517b2485e0ca577a6b540818f29cb0
-SIZE (biopython-1.48.tar.gz) = 4149100
+MD5 (biopython-1.51.tar.gz) = e973cb96b44b47526d31b6a0039c686f
+SHA256 (biopython-1.51.tar.gz) = 0ebf44e6376d7b44fb2857e751d388f30402d6a81798821e40a7f7b92a4b036b
+SIZE (biopython-1.51.tar.gz) = 5557548
diff --git a/biology/py-biopython/files/patch-setup.py b/biology/py-biopython/files/patch-setup.py
deleted file mode 100644
index aa8efc1fcd9d..000000000000
--- a/biology/py-biopython/files/patch-setup.py
+++ /dev/null
@@ -1,34 +0,0 @@
---- setup.py.orig	Sat Mar 17 13:21:04 2007
-+++ setup.py	Mon May 28 17:01:45 2007
-@@ -112,7 +112,7 @@
-         
-     
-     # Compile KDTree ? Not compiled by default
--    print "\n*** Bio.KDTree *** NOT built by default "
-+#    print "\n*** Bio.KDTree *** NOT built by default "
-     kdtree_msg = """
- The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module,
- which in turn, depends on C++ code that does not compile cleanly on
-@@ -120,14 +120,14 @@
- 
- Would you like to build Bio.KDTree ?"""
- 
--    if get_yes_or_no (kdtree_msg, 0):
--        NUMPY_PACKAGES.append("Bio.KDTree")
--        NUMPY_EXTENSIONS.append(
--            CplusplusExtension('Bio.KDTree._CKDTree', 
--                               ["Bio/KDTree/KDTree.cpp",
--                                "Bio/KDTree/KDTree.swig.cpp"],
--                               libraries=["stdc++"],
--                               language="c++"))
-+#    if get_yes_or_no (kdtree_msg, 0):
-+    NUMPY_PACKAGES.append("Bio.KDTree")
-+    NUMPY_EXTENSIONS.append(
-+        CplusplusExtension('Bio.KDTree._CKDTree', 
-+                           ["Bio/KDTree/KDTree.cpp",
-+                            "Bio/KDTree/KDTree.swig.cpp"],
-+                           libraries=["stdc++"],
-+                           language="c++"))
-     
-     
-     return 1
diff --git a/biology/py-biopython/pkg-plist b/biology/py-biopython/pkg-plist
index 2d884d98248f..6380a04f71ac 100644
--- a/biology/py-biopython/pkg-plist
+++ b/biology/py-biopython/pkg-plist
@@ -1,15 +1,52 @@
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.py
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyo
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.py
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyo
+%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.py
+%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyo
+%%PYTHON_SITELIBDIR%%/BioSQL/Loader.py
+%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyo
+%%PYTHON_SITELIBDIR%%/BioSQL/__init__.py
+%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyc
+%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyo
+@dirrm %%PYTHON_SITELIBDIR%%/BioSQL
 %%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.py
 %%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Affy/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Affy/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Affy/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Ais/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/Ais/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Ais/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Align/AlignInfo.py
 %%PYTHON_SITELIBDIR%%/Bio/Align/AlignInfo.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Align/AlignInfo.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Clustalw.py
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Clustalw.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Clustalw.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Dialign.py
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Dialign.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Dialign.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Mafft.py
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Mafft.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Mafft.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Muscle.py
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Muscle.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Muscle.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Prank.py
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Prank.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Prank.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Probcons.py
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Probcons.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Probcons.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_TCoffee.py
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_TCoffee.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_TCoffee.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Align/FormatConvert.py
 %%PYTHON_SITELIBDIR%%/Bio/Align/FormatConvert.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Align/FormatConvert.pyo
@@ -100,15 +137,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/CAPS/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/CAPS/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/CAPS/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/CDD/Record.py
-%%PYTHON_SITELIBDIR%%/Bio/CDD/Record.pyc
-%%PYTHON_SITELIBDIR%%/Bio/CDD/Record.pyo
-%%PYTHON_SITELIBDIR%%/Bio/CDD/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/CDD/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/CDD/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/CDD/cdd_format.py
-%%PYTHON_SITELIBDIR%%/Bio/CDD/cdd_format.pyc
-%%PYTHON_SITELIBDIR%%/Bio/CDD/cdd_format.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Clustalw/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Clustalw/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Clustalw/__init__.pyo
@@ -122,9 +150,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/Crystal/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Crystal/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Crystal/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/DBXRef.py
-%%PYTHON_SITELIBDIR%%/Bio/DBXRef.pyc
-%%PYTHON_SITELIBDIR%%/Bio/DBXRef.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Data/CodonTable.py
 %%PYTHON_SITELIBDIR%%/Bio/Data/CodonTable.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Data/CodonTable.pyo
@@ -134,21 +159,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/Data/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Data/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Data/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Decode.py
-%%PYTHON_SITELIBDIR%%/Bio/Decode.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Decode.pyo
 %%PYTHON_SITELIBDIR%%/Bio/DocSQL.py
 %%PYTHON_SITELIBDIR%%/Bio/DocSQL.pyc
 %%PYTHON_SITELIBDIR%%/Bio/DocSQL.pyo
-%%PYTHON_SITELIBDIR%%/Bio/ECell/Record.py
-%%PYTHON_SITELIBDIR%%/Bio/ECell/Record.pyc
-%%PYTHON_SITELIBDIR%%/Bio/ECell/Record.pyo
-%%PYTHON_SITELIBDIR%%/Bio/ECell/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/ECell/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/ECell/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/ECell/ecell_format.py
-%%PYTHON_SITELIBDIR%%/Bio/ECell/ecell_format.pyc
-%%PYTHON_SITELIBDIR%%/Bio/ECell/ecell_format.pyo
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/Config.py
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/Config.pyc
 %%PYTHON_SITELIBDIR%%/Bio/EUtils/Config.pyo
@@ -224,9 +237,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.py
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer.py
-%%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer3.py
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer3.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer3.pyo
@@ -236,23 +246,16 @@
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Emboss/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Emboss/primer3_format.py
-%%PYTHON_SITELIBDIR%%/Bio/Emboss/primer3_format.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Emboss/primer3_format.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Emboss/primersearch_format.py
-%%PYTHON_SITELIBDIR%%/Bio/Emboss/primersearch_format.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Emboss/primersearch_format.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Encodings/IUPACEncoding.py
 %%PYTHON_SITELIBDIR%%/Bio/Encodings/IUPACEncoding.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Encodings/IUPACEncoding.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Encodings/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Encodings/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Encodings/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Entrez/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/Entrez/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Entrez/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/EMBL_General.mod.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/GenBank_General.mod.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/HomoloGene.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/HomoloGene.mod.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd
@@ -293,20 +296,41 @@
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eSummary_041029.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/egquery.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmcommon_080101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmcommon_090101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedline_080101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedline_090101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmserials_080101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_080101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_090101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/taxon.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/Parser.py
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/Parser.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/Parser.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Entrez/SerialSet.py
-%%PYTHON_SITELIBDIR%%/Bio/Entrez/SerialSet.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Entrez/SerialSet.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Enzyme/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Enzyme/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Enzyme/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Enzyme.py
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Enzyme.pyc
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Enzyme.pyo
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Prodoc.py
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Prodoc.pyc
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Prodoc.pyo
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Prosite.py
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Prosite.pyc
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Prosite.pyo
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/ScanProsite.py
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/ScanProsite.pyc
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/ScanProsite.pyo
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/ExPASy/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/FSSP/FSSPTools.py
 %%PYTHON_SITELIBDIR%%/Bio/FSSP/FSSPTools.pyc
 %%PYTHON_SITELIBDIR%%/Bio/FSSP/FSSPTools.pyo
@@ -418,9 +442,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/Geo/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Geo/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Geo/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Gobase/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/Gobase/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Gobase/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Graphics/BasicChromosome.py
 %%PYTHON_SITELIBDIR%%/Bio/Graphics/BasicChromosome.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Graphics/BasicChromosome.pyo
@@ -433,6 +454,39 @@
 %%PYTHON_SITELIBDIR%%/Bio/Graphics/Distribution.py
 %%PYTHON_SITELIBDIR%%/Bio/Graphics/Distribution.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Graphics/Distribution.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_AbstractDrawer.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_AbstractDrawer.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_CircularDrawer.py
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_CircularDrawer.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_CircularDrawer.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Colors.py
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Colors.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Colors.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Diagram.py
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Diagram.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Diagram.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Feature.py
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Feature.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Feature.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_FeatureSet.py
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_FeatureSet.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_FeatureSet.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Graph.py
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Graph.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Graph.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_GraphSet.py
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_GraphSet.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_GraphSet.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_LinearDrawer.py
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_LinearDrawer.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_LinearDrawer.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Track.py
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Track.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Track.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/__init__.pyo
 %%PYTHON_SITELIBDIR%%/Bio/Graphics/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/Graphics/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Graphics/__init__.pyo
@@ -457,21 +511,9 @@
 %%PYTHON_SITELIBDIR%%/Bio/Index.py
 %%PYTHON_SITELIBDIR%%/Bio/Index.pyc
 %%PYTHON_SITELIBDIR%%/Bio/Index.pyo
-%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/Record.py
-%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/Record.pyc
-%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/Record.pyo
-%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/intelligenetics_format.py
-%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/intelligenetics_format.pyc
-%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/intelligenetics_format.pyo
 %%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/KDTree/CKDTree.py
-%%PYTHON_SITELIBDIR%%/Bio/KDTree/CKDTree.pyc
-%%PYTHON_SITELIBDIR%%/Bio/KDTree/CKDTree.pyo
 %%PYTHON_SITELIBDIR%%/Bio/KDTree/KDTree.py
 %%PYTHON_SITELIBDIR%%/Bio/KDTree/KDTree.pyc
 %%PYTHON_SITELIBDIR%%/Bio/KDTree/KDTree.pyo
@@ -491,15 +533,6 @@
 %%PYTHON_SITELIBDIR%%/Bio/KEGG/__init__.py
 %%PYTHON_SITELIBDIR%%/Bio/KEGG/__init__.pyc
 %%PYTHON_SITELIBDIR%%/Bio/KEGG/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/LocusLink/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/LocusLink/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/LocusLink/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/LocusLink/locus_format.py
-%%PYTHON_SITELIBDIR%%/Bio/LocusLink/locus_format.pyc
-%%PYTHON_SITELIBDIR%%/Bio/LocusLink/locus_format.pyo
-%%PYTHON_SITELIBDIR%%/Bio/LocusLink/web_parse.py
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-%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/ipi.pyo
-%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/speclist.py
-%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/speclist.pyc
-%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/speclist.pyo
-%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/sprot38.py
-%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/sprot38.pyc
-%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/sprot38.pyo
-%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/sprot40.py
-%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/sprot40.pyc
-%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/sprot40.pyo
-%%PYTHON_SITELIBDIR%%/Bio/expressions/transfac.py
-%%PYTHON_SITELIBDIR%%/Bio/expressions/transfac.pyc
-%%PYTHON_SITELIBDIR%%/Bio/expressions/transfac.pyo
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/embl.py
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/embl.pyc
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/embl.pyo
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/genbank.py
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/genbank.pyc
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/genbank.pyo
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/search.py
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/search.pyc
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/search.pyo
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/sequence.py
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/sequence.pyc
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/sequence.pyo
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.py
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.pyc
-%%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.pyo
-%%PYTHON_SITELIBDIR%%/Bio/ExPASy.py
-%%PYTHON_SITELIBDIR%%/Bio/ExPASy.pyc
-%%PYTHON_SITELIBDIR%%/Bio/ExPASy.pyo
 %%PYTHON_SITELIBDIR%%/Bio/kNN.py
 %%PYTHON_SITELIBDIR%%/Bio/kNN.pyc
 %%PYTHON_SITELIBDIR%%/Bio/kNN.pyo
@@ -1200,83 +1038,8 @@
 %%PYTHON_SITELIBDIR%%/Bio/utils.py
 %%PYTHON_SITELIBDIR%%/Bio/utils.pyc
 %%PYTHON_SITELIBDIR%%/Bio/utils.pyo
-%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/embl.py
-%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/embl.pyc
-%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/embl.pyo
-%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/empty.py
-%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/empty.pyc
-%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/empty.pyo
-%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/fasta.py
-%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/fasta.pyc
-%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/fasta.pyo
-%%PYTHON_SITELIBDIR%%/Bio/writers/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/writers/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/writers/__init__.pyo
-%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.py
-%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyc
-%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyo
-%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.py
-%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyc
-%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyo
-%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.py
-%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyc
-%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyo
-%%PYTHON_SITELIBDIR%%/BioSQL/Loader.py
-%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyc
-%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyo
-%%PYTHON_SITELIBDIR%%/BioSQL/__init__.py
-%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyc
-%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Martel/Dispatch.py
-%%PYTHON_SITELIBDIR%%/Martel/Dispatch.pyc
-%%PYTHON_SITELIBDIR%%/Martel/Dispatch.pyo
-%%PYTHON_SITELIBDIR%%/Martel/Expression.py
-%%PYTHON_SITELIBDIR%%/Martel/Expression.pyc
-%%PYTHON_SITELIBDIR%%/Martel/Expression.pyo
-%%PYTHON_SITELIBDIR%%/Martel/Generate.py
-%%PYTHON_SITELIBDIR%%/Martel/Generate.pyc
-%%PYTHON_SITELIBDIR%%/Martel/Generate.pyo
-%%PYTHON_SITELIBDIR%%/Martel/IterParser.py
-%%PYTHON_SITELIBDIR%%/Martel/IterParser.pyc
-%%PYTHON_SITELIBDIR%%/Martel/IterParser.pyo
-%%PYTHON_SITELIBDIR%%/Martel/Iterator.py
-%%PYTHON_SITELIBDIR%%/Martel/Iterator.pyc
-%%PYTHON_SITELIBDIR%%/Martel/Iterator.pyo
-%%PYTHON_SITELIBDIR%%/Martel/LAX.py
-%%PYTHON_SITELIBDIR%%/Martel/LAX.pyc
-%%PYTHON_SITELIBDIR%%/Martel/LAX.pyo
-%%PYTHON_SITELIBDIR%%/Martel/Parser.py
-%%PYTHON_SITELIBDIR%%/Martel/Parser.pyc
-%%PYTHON_SITELIBDIR%%/Martel/Parser.pyo
-%%PYTHON_SITELIBDIR%%/Martel/RecordReader.py
-%%PYTHON_SITELIBDIR%%/Martel/RecordReader.pyc
-%%PYTHON_SITELIBDIR%%/Martel/RecordReader.pyo
-%%PYTHON_SITELIBDIR%%/Martel/Time.py
-%%PYTHON_SITELIBDIR%%/Martel/Time.pyc
-%%PYTHON_SITELIBDIR%%/Martel/Time.pyo
-%%PYTHON_SITELIBDIR%%/Martel/__init__.py
-%%PYTHON_SITELIBDIR%%/Martel/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Martel/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Martel/convert_re.py
-%%PYTHON_SITELIBDIR%%/Martel/convert_re.pyc
-%%PYTHON_SITELIBDIR%%/Martel/convert_re.pyo
-%%PYTHON_SITELIBDIR%%/Martel/msre_constants.py
-%%PYTHON_SITELIBDIR%%/Martel/msre_constants.pyc
-%%PYTHON_SITELIBDIR%%/Martel/msre_constants.pyo
-%%PYTHON_SITELIBDIR%%/Martel/msre_parse.py
-%%PYTHON_SITELIBDIR%%/Martel/msre_parse.pyc
-%%PYTHON_SITELIBDIR%%/Martel/msre_parse.pyo
-%%PYTHON_SITELIBDIR%%/Martel/optimize.py
-%%PYTHON_SITELIBDIR%%/Martel/optimize.pyc
-%%PYTHON_SITELIBDIR%%/Martel/optimize.pyo
-%%PYTHON_SITELIBDIR%%/Martel/setup.py
-%%PYTHON_SITELIBDIR%%/Martel/setup.pyc
-%%PYTHON_SITELIBDIR%%/Martel/setup.pyo
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Affy
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Ais
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Align/Applications
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Align
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignAce
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignIO
@@ -1284,20 +1047,19 @@
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Application
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Blast
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/CAPS
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/CDD
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Clustalw
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Cluster
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Compass
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Crystal
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Data
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/ECell
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/EUtils
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Emboss
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Encodings
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Entrez
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Enzyme
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/ExPASy
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/FSSP
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Fasta
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Crossover
@@ -1308,46 +1070,42 @@
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/GFF
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/GenBank
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Geo
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Gobase
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Graphics
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/HMM
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/InterPro
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/KDTree
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Map
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/LocusLink
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/MEME
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Medline
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/MetaTool
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Mindy
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/NBRF
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Motif/Applications
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Motif
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/NMR
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Ndb
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/BackPropagation
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/Gene
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Nexus
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/PDB/mmCIF
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/PDB
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Parsers
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway/Rep
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal
+@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Prosite
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Rebase
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Restriction/_Update
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Restriction
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/SCOP
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Saf
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqIO
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqUtils
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Sequencing
@@ -1357,18 +1115,4 @@
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/UniGene
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/WWW
 @dirrm %%PYTHON_SITELIBDIR%%/Bio/Wise
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/Search
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/builders
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/config
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/dbdefs
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/blast
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/embl
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/formatdefs
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord
-@dirrm %%PYTHON_SITELIBDIR%%/Bio/writers
 @dirrm %%PYTHON_SITELIBDIR%%/Bio
-@dirrm %%PYTHON_SITELIBDIR%%/BioSQL
-@dirrm %%PYTHON_SITELIBDIR%%/Martel