UPDATE: biology/py-biopython

Sat, 26 Jan 2013 07:38:16 -0800 

Hi,

This diff updates py-biopython to the latest release 1.60.
Tested on amd64, maintainer timeout.

Comments ? OK ?

Cheers,
benoit

Index: Makefile
===================================================================
RCS file: /cvs/ports/biology/py-biopython/Makefile,v
retrieving revision 1.20
diff -u -r1.20 Makefile
--- Makefile	1 Nov 2011 16:05:26 -0000	1.20
+++ Makefile	4 Jan 2013 21:50:24 -0000
@@ -3,9 +3,9 @@
 SHARED_ONLY=		Yes
 COMMENT=		Python tools for computational molecular biology
 
-MODPY_EGG_VERSION=	1.50
+MODPY_EGG_VERSION=	1.60
 DISTNAME=		biopython-${MODPY_EGG_VERSION}
-REVISION =		3
+PKGNAME =		py-${DISTNAME}
 CATEGORIES=		biology
 
 HOMEPAGE=		http://www.biopython.org/
Index: distinfo
===================================================================
RCS file: /cvs/ports/biology/py-biopython/distinfo,v
retrieving revision 1.6
diff -u -r1.6 distinfo
--- distinfo	2 Jun 2009 04:48:32 -0000	1.6
+++ distinfo	4 Jan 2013 21:50:24 -0000
@@ -1,5 +1,2 @@
-MD5 (biopython-1.50.tar.gz) = OykYeEa6oiPHwaTpoFjmuQ==
-RMD160 (biopython-1.50.tar.gz) = VDwYfwVqCrr+MBkEYPp17lOw0DY=
-SHA1 (biopython-1.50.tar.gz) = 3nr+5QM3W4yPiXudcidsBJpzwNU=
-SHA256 (biopython-1.50.tar.gz) = ek0yqDhBFZ6RLHkUs1+04Xzc9Eeugmb+WzG1o6SV14M=
-SIZE (biopython-1.50.tar.gz) = 4660143
+SHA256 (biopython-1.60.tar.gz) = c6Lm1wDIc1gytvwV3QipuqQTawcv8YdgudIvVjV51zM=
+SIZE (biopython-1.60.tar.gz) = 9501707
Index: patches/patch-Tests_run_tests_py
===================================================================
RCS file: /cvs/ports/biology/py-biopython/patches/patch-Tests_run_tests_py,v
retrieving revision 1.3
diff -u -r1.3 patch-Tests_run_tests_py
--- patches/patch-Tests_run_tests_py	2 Jun 2009 04:48:32 -0000	1.3
+++ patches/patch-Tests_run_tests_py	4 Jan 2013 21:50:24 -0000
@@ -1,7 +1,7 @@
-$OpenBSD: patch-Tests_run_tests_py,v 1.3 2009/06/02 04:48:32 wcmaier Exp $
---- Tests/run_tests.py.orig	Thu Apr 16 04:37:26 2009
-+++ Tests/run_tests.py	Mon Jun  1 21:17:37 2009
-@@ -65,11 +65,11 @@ def main(argv):
+$OpenBSD$
+--- Tests/run_tests.py.orig	Mon Jun 25 11:10:25 2012
++++ Tests/run_tests.py	Fri Jan  4 22:03:19 2013
+@@ -131,11 +131,11 @@
      # A. Because Martel may not be in ../build/lib.*
      test_path = sys.path[0] or "."
      source_path = os.path.abspath("%s/.." % test_path)
@@ -13,6 +13,6 @@
 -        sys.path.insert(1, build_path)
 +    #if os.access(build_path, os.F_OK):
 +    #    sys.path.insert(1, build_path)
-     
-     # get the command line options
-     try:
+ 
+     # Using "export LANG=C" (which should work on Linux and similar) can
+     # avoid problems detecting optional command line tools on
Index: pkg/PLIST
===================================================================
RCS file: /cvs/ports/biology/py-biopython/pkg/PLIST,v
retrieving revision 1.7
diff -u -r1.7 PLIST
--- pkg/PLIST	2 Jun 2009 04:48:32 -0000	1.7
+++ pkg/PLIST	4 Jan 2013 21:50:24 -0000
@@ -1,4 +1,8 @@
 @comment $OpenBSD: PLIST,v 1.7 2009/06/02 04:48:32 wcmaier Exp $
+@comment lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/setup.py
+@comment lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/setup.pyc
+@comment lib/python${MODPY_VERSION}/site-packages/Martel/setup.py
+@comment lib/python${MODPY_VERSION}/site-packages/Martel/setup.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/
 lib/python${MODPY_VERSION}/site-packages/Bio/Affy/
 lib/python${MODPY_VERSION}/site-packages/Bio/Affy/CelFile.py
@@ -8,27 +12,29 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/AlignInfo.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/AlignInfo.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Align/FormatConvert.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Align/FormatConvert.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_ClustalOmega.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_ClustalOmega.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Clustalw.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Clustalw.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Dialign.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Dialign.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Mafft.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Mafft.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Muscle.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Muscle.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Prank.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Prank.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Probcons.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_Probcons.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_TCoffee.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/_TCoffee.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/__init__.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/Applications/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/Generic.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/Generic.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/AlignAceStandalone.py
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/AlignAceStandalone.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/Applications.py
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/Applications.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/CompareAceStandalone.py
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/CompareAceStandalone.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/Motif.py
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/Motif.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/Parser.py
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/Parser.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/Scanner.py
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/Scanner.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/AlignAce/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/AlignIO/
 lib/python${MODPY_VERSION}/site-packages/Bio/AlignIO/ClustalIO.py
 lib/python${MODPY_VERSION}/site-packages/Bio/AlignIO/ClustalIO.pyc
@@ -74,9 +80,6 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/CAPS/
 lib/python${MODPY_VERSION}/site-packages/Bio/CAPS/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/CAPS/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Clustalw/
-lib/python${MODPY_VERSION}/site-packages/Bio/Clustalw/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Clustalw/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/
 lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Cluster/__init__.pyc
@@ -87,8 +90,6 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/Crystal/
 lib/python${MODPY_VERSION}/site-packages/Bio/Crystal/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Crystal/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/DBXRef.py
-lib/python${MODPY_VERSION}/site-packages/Bio/DBXRef.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Data/
 lib/python${MODPY_VERSION}/site-packages/Bio/Data/CodonTable.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Data/CodonTable.pyc
@@ -96,82 +97,17 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/Data/IUPACData.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Data/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Data/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Decode.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Decode.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/DocSQL.py
 lib/python${MODPY_VERSION}/site-packages/Bio/DocSQL.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/Config.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/Config.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DBIdsClient.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DBIdsClient.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/LinkOut.dtd
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/LinkOut.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/LinkOut.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/eInfo_020511.dtd
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/eInfo_020511.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/eInfo_020511.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/eLink_020511.dtd
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/eLink_020511.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/eLink_020511.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/ePost_020511.dtd
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/ePost_020511.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/ePost_020511.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/eSearch_020511.dtd
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/eSearch_020511.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/eSearch_020511.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/eSummary_020511.dtd
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/eSummary_020511.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/DTDs/eSummary_020511.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/Datatypes.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/Datatypes.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/HistoryClient.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/HistoryClient.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/Mixins.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/Mixins.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/MultiDict.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/MultiDict.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/POM.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/POM.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/ReseekFile.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/ReseekFile.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/ThinClient.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/ThinClient.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/dtd2py.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/dtd2py.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/parse.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/parse.pyc
-@comment lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/setup.py
-@comment lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/setup.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/sourcegen.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EUtils/sourcegen.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/EZRetrieve.py
-lib/python${MODPY_VERSION}/site-packages/Bio/EZRetrieve.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/
 lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/Applications.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/Applications.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/Primer.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/Primer.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/Primer3.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/Primer3.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/PrimerSearch.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/PrimerSearch.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/primer3_format.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/primer3_format.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/primersearch_format.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Emboss/primersearch_format.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Encodings/
-lib/python${MODPY_VERSION}/site-packages/Bio/Encodings/IUPACEncoding.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Encodings/IUPACEncoding.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Encodings/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Encodings/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/EMBL_General.mod.dtd
@@ -180,6 +116,8 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/HomoloGene.mod.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd
@@ -210,32 +148,103 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/PIR_General.mod.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/PRF_General.mod.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/SP_General.mod.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/XHTMLtablesetup.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/archivearticle.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/archivecustom-classes.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/archivecustom-mixes.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/archivecustom-models.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/archivecustom-modules.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/articlemeta.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/backmatter.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/bookdoc_100301.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/bookdoc_110101.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/bookdoc_120101.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/chars.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/common.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/default-classes.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/default-mixes.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/display.ent
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/eInfo_020511.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/eLink_020511.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/eLink_090910.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/eLink_101123.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/ePost_020511.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/eSearch_020511.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/eSpell.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/eSummary_041029.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/egquery.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/elink_020122.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/format.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/htmltable.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isoamsa.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isoamsb.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isoamsc.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isoamsn.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isoamso.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isoamsr.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isobox.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isocyr1.ent
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+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isolat1.ent
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+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isomfrk.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isomopf.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isomscr.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isonum.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isopub.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/isotech.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/journalmeta.ent
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+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/mmlextra.ent
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 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/nlmcommon_080101.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/nlmcommon_090101.dtd
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 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/nlmmedline_080101.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/nlmmedline_090101.dtd
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 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/nlmserials_080101.dtd
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+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/notat.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/para.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/phrase.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/pmc-1.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/pubmed_020114.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/pubmed_080101.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/pubmed_090101.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/pubmed_100101.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/pubmed_100301.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/pubmed_110101.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/pubmed_120101.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/references.ent
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/section.ent
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/taxon.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/xmlspecchars.ent
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/Parser.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/Parser.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Enzyme/
-lib/python${MODPY_VERSION}/site-packages/Bio/Enzyme/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Enzyme/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/ExPASy/
 lib/python${MODPY_VERSION}/site-packages/Bio/ExPASy/Enzyme.py
 lib/python${MODPY_VERSION}/site-packages/Bio/ExPASy/Enzyme.pyc
@@ -254,15 +263,8 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/fssp_rec.py
 lib/python${MODPY_VERSION}/site-packages/Bio/FSSP/fssp_rec.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Fasta/
-lib/python${MODPY_VERSION}/site-packages/Bio/Fasta/FastaAlign.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Fasta/FastaAlign.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Fasta/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Fasta/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/File.py
 lib/python${MODPY_VERSION}/site-packages/Bio/File.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/FilteredReader.py
-lib/python${MODPY_VERSION}/site-packages/Bio/FilteredReader.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/GA/
 lib/python${MODPY_VERSION}/site-packages/Bio/GA/Crossover/
 lib/python${MODPY_VERSION}/site-packages/Bio/GA/Crossover/General.py
@@ -306,18 +308,7 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/GA/Selection/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/GA/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/GA/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/GFF/
-lib/python${MODPY_VERSION}/site-packages/Bio/GFF/GenericTools.py
-lib/python${MODPY_VERSION}/site-packages/Bio/GFF/GenericTools.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/GFF/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/GFF/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/GFF/binning.py
-lib/python${MODPY_VERSION}/site-packages/Bio/GFF/binning.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/GFF/easy.py
-lib/python${MODPY_VERSION}/site-packages/Bio/GFF/easy.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/
-lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/LocationParser.py
-lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/LocationParser.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/Record.py
 lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/Record.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/GenBank/Scanner.py
@@ -347,6 +338,8 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/GenomeDiagram/_Colors.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/GenomeDiagram/_Colors.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/GenomeDiagram/_CrossLink.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/GenomeDiagram/_Diagram.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/GenomeDiagram/_Diagram.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Graphics/GenomeDiagram/_Feature.py
@@ -380,16 +373,6 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/HotRand.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Index.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Index.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/
-lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/Record.py
-lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/Record.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/intelligenetics_format.py
-lib/python${MODPY_VERSION}/site-packages/Bio/IntelliGenetics/intelligenetics_format.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/InterPro/
-lib/python${MODPY_VERSION}/site-packages/Bio/InterPro/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/InterPro/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/
 lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/KDTree.py
 lib/python${MODPY_VERSION}/site-packages/Bio/KDTree/KDTree.pyc
@@ -410,13 +393,6 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/KEGG/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/LogisticRegression.py
 lib/python${MODPY_VERSION}/site-packages/Bio/LogisticRegression.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/MEME/
-lib/python${MODPY_VERSION}/site-packages/Bio/MEME/Motif.py
-lib/python${MODPY_VERSION}/site-packages/Bio/MEME/Motif.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/MEME/Parser.py
-lib/python${MODPY_VERSION}/site-packages/Bio/MEME/Parser.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/MEME/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/MEME/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/MarkovModel.py
 lib/python${MODPY_VERSION}/site-packages/Bio/MarkovModel.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/MaxEntropy.py
@@ -424,36 +400,17 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/Medline/
 lib/python${MODPY_VERSION}/site-packages/Bio/Medline/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Medline/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/
-lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/Input.py
-lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/Input.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/Record.py
-lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/Record.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/metatool_format.py
-lib/python${MODPY_VERSION}/site-packages/Bio/MetaTool/metatool_format.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/BaseDB.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/BaseDB.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/BerkeleyDB.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/BerkeleyDB.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/FlatDB.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/FlatDB.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/Location.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/Location.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/SimpleSeqRecord.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/SimpleSeqRecord.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/XPath.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/XPath.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/compression.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Mindy/compression.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Motif/
+lib/python${MODPY_VERSION}/site-packages/Bio/Motif/Applications/
+lib/python${MODPY_VERSION}/site-packages/Bio/Motif/Applications/_AlignAce.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Motif/Applications/_AlignAce.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Motif/Applications/__init__.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Motif/Applications/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Motif/Parsers/
 lib/python${MODPY_VERSION}/site-packages/Bio/Motif/Parsers/AlignAce.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Motif/Parsers/AlignAce.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Motif/Parsers/MAST.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Motif/Parsers/MAST.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Motif/Parsers/MEME.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Motif/Parsers/MEME.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Motif/Parsers/__init__.py
@@ -464,15 +421,7 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/Motif/_Motif.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Motif/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Motif/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/
-lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/Record.py
-lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/Record.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/ValSeq.py
-lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/ValSeq.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/nbrf_format.py
-lib/python${MODPY_VERSION}/site-packages/Bio/NBRF/nbrf_format.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Motif/_pwm.so
 lib/python${MODPY_VERSION}/site-packages/Bio/NMR/
 lib/python${MODPY_VERSION}/site-packages/Bio/NMR/NOEtools.py
 lib/python${MODPY_VERSION}/site-packages/Bio/NMR/NOEtools.pyc
@@ -482,11 +431,6 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/NMR/xpktools.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/NaiveBayes.py
 lib/python${MODPY_VERSION}/site-packages/Bio/NaiveBayes.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Ndb/
-lib/python${MODPY_VERSION}/site-packages/Bio/Ndb/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Ndb/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/NetCatch.py
-lib/python${MODPY_VERSION}/site-packages/Bio/NetCatch.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/
 lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/BackPropagation/
 lib/python${MODPY_VERSION}/site-packages/Bio/NeuralNetwork/BackPropagation/Layer.py
@@ -580,17 +524,13 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/
+lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/MMCIFlex.so
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/mmCIF/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/parse_pdb_header.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/parse_pdb_header.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/ParserSupport.py
 lib/python${MODPY_VERSION}/site-packages/Bio/ParserSupport.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Parsers/
-lib/python${MODPY_VERSION}/site-packages/Bio/Parsers/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Parsers/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Parsers/spark.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Parsers/spark.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/
 lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/Rep/
 lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/Rep/Graph.py
@@ -603,6 +543,53 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/Rep/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Pathway/__init__.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/Applications/
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/Applications/_Phyml.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/Applications/_Phyml.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/Applications/_Raxml.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/Applications/_Raxml.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/Applications/__init__.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/Applications/__init__.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/BaseTree.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/BaseTree.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/Newick.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/Newick.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/NewickIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/NewickIO.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/NexusIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/NexusIO.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/__init__.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/__init__.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/_paml.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/_paml.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/_parse_baseml.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/_parse_baseml.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/_parse_codeml.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/_parse_codeml.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/_parse_yn00.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/_parse_yn00.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/baseml.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/baseml.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/chi2.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/chi2.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/codeml.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/codeml.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/yn00.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PAML/yn00.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PhyloXML.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PhyloXML.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PhyloXMLIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/PhyloXMLIO.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/__init__.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/__init__.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/_io.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/_io.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/_sugar.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/_sugar.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/_utils.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Phylo/_utils.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/
 lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/Async/
 lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/Async/Local.py
@@ -619,6 +606,14 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/FDist/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/Controller.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/Controller.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/EasyController.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/EasyController.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/FileParser.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/FileParser.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/LargeFileParser.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/LargeFileParser.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/Utils.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/Utils.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/GenePop/__init__.py
@@ -647,19 +642,7 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/SimCoal/data/ssm_2d.par
 lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PopGen/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/PropertyManager.py
-lib/python${MODPY_VERSION}/site-packages/Bio/PropertyManager.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/
-lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/Pattern.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/Pattern.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/Prodoc.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/Prodoc.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Prosite/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/PubMed.py
-lib/python${MODPY_VERSION}/site-packages/Bio/PubMed.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Restriction/
-lib/python${MODPY_VERSION}/site-packages/Bio/Restriction/DNAUtils.so
 lib/python${MODPY_VERSION}/site-packages/Bio/Restriction/PrintFormat.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Restriction/PrintFormat.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Restriction/RanaConfig.py
@@ -684,8 +667,6 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/Des.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/Dom.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/Dom.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/FileIndex.py
-lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/FileIndex.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/Hie.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/Hie.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/Raf.py
@@ -694,18 +675,13 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/Residues.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/__init__.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/three_to_one_dict.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SCOP/three_to_one_dict.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/
 lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/SVDSuperimposer.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/SVDSuperimposer.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SVDSuperimposer/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Saf/
-lib/python${MODPY_VERSION}/site-packages/Bio/Saf/Record.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Saf/Record.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Saf/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Saf/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Saf/saf_format.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Saf/saf_format.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Search.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Search.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Seq.py
@@ -713,6 +689,8 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqFeature.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqFeature.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/AbiIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/AbiIO.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/AceIO.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/AceIO.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/FastaIO.py
@@ -729,12 +707,22 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/PirIO.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/QualityIO.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/QualityIO.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/SeqXmlIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/SeqXmlIO.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/SffIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/SffIO.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/SwissIO.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/SwissIO.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/TabIO.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/TabIO.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/UniprotIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/UniprotIO.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/__init__.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/_convert.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/_convert.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/_index.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/_index.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqRecord.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqRecord.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqUtils/
@@ -759,6 +747,11 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/
 lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Ace.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Ace.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Applications/
+lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Applications/_Novoalign.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Applications/_Novoalign.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Applications/__init__.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Applications/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Phd.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/Phd.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Sequencing/__init__.py
@@ -768,10 +761,6 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/Statistics/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Statistics/lowess.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Statistics/lowess.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Std.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Std.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/StdHandler.py
-lib/python${MODPY_VERSION}/site-packages/Bio/StdHandler.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SubsMat/
 lib/python${MODPY_VERSION}/site-packages/Bio/SubsMat/FreqTable.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SubsMat/FreqTable.pyc
@@ -782,20 +771,16 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/SwissProt/
 lib/python${MODPY_VERSION}/site-packages/Bio/SwissProt/KeyWList.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SwissProt/KeyWList.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/SwissProt/SProt.py
-lib/python${MODPY_VERSION}/site-packages/Bio/SwissProt/SProt.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SwissProt/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SwissProt/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Transcribe.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Transcribe.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Translate.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Translate.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/TogoWS/
+lib/python${MODPY_VERSION}/site-packages/Bio/TogoWS/__init__.py
+lib/python${MODPY_VERSION}/site-packages/Bio/TogoWS/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/UniGene/
+lib/python${MODPY_VERSION}/site-packages/Bio/UniGene/UniGene.py
+lib/python${MODPY_VERSION}/site-packages/Bio/UniGene/UniGene.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/UniGene/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/UniGene/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/WWW/
-lib/python${MODPY_VERSION}/site-packages/Bio/WWW/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/WWW/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Wise/
 lib/python${MODPY_VERSION}/site-packages/Bio/Wise/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Wise/__init__.pyc
@@ -803,44 +788,20 @@
 lib/python${MODPY_VERSION}/site-packages/Bio/Wise/dnal.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Wise/psw.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Wise/psw.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Writer.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Writer.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/__init__.py
 lib/python${MODPY_VERSION}/site-packages/Bio/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/cMarkovModel.so
-lib/python${MODPY_VERSION}/site-packages/Bio/clistfns.so
-lib/python${MODPY_VERSION}/site-packages/Bio/cmathfns.so
+lib/python${MODPY_VERSION}/site-packages/Bio/_py3k.py
+lib/python${MODPY_VERSION}/site-packages/Bio/_py3k.pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/bgzf.py
+lib/python${MODPY_VERSION}/site-packages/Bio/bgzf.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/cpairwise2.so
-lib/python${MODPY_VERSION}/site-packages/Bio/cstringfns.so
-lib/python${MODPY_VERSION}/site-packages/Bio/distance.py
-lib/python${MODPY_VERSION}/site-packages/Bio/distance.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/kNN.py
 lib/python${MODPY_VERSION}/site-packages/Bio/kNN.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/listfns.py
-lib/python${MODPY_VERSION}/site-packages/Bio/listfns.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/mathfns.py
-lib/python${MODPY_VERSION}/site-packages/Bio/mathfns.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/pairwise2.py
 lib/python${MODPY_VERSION}/site-packages/Bio/pairwise2.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/stringfns.py
-lib/python${MODPY_VERSION}/site-packages/Bio/stringfns.pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/trie.so
 lib/python${MODPY_VERSION}/site-packages/Bio/triefind.py
 lib/python${MODPY_VERSION}/site-packages/Bio/triefind.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/utils.py
-lib/python${MODPY_VERSION}/site-packages/Bio/utils.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/writers/
-lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/
-lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/embl.py
-lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/embl.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/empty.py
-lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/empty.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/fasta.py
-lib/python${MODPY_VERSION}/site-packages/Bio/writers/SeqRecord/fasta.pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/writers/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Bio/writers/__init__.pyc
 lib/python${MODPY_VERSION}/site-packages/BioSQL/
 lib/python${MODPY_VERSION}/site-packages/BioSQL/BioSeq.py
 lib/python${MODPY_VERSION}/site-packages/BioSQL/BioSeq.pyc
@@ -852,59 +813,31 @@
 lib/python${MODPY_VERSION}/site-packages/BioSQL/Loader.pyc
 lib/python${MODPY_VERSION}/site-packages/BioSQL/__init__.py
 lib/python${MODPY_VERSION}/site-packages/BioSQL/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Martel/
-lib/python${MODPY_VERSION}/site-packages/Martel/Dispatch.py
-lib/python${MODPY_VERSION}/site-packages/Martel/Dispatch.pyc
-lib/python${MODPY_VERSION}/site-packages/Martel/Expression.py
-lib/python${MODPY_VERSION}/site-packages/Martel/Expression.pyc
-lib/python${MODPY_VERSION}/site-packages/Martel/Generate.py
-lib/python${MODPY_VERSION}/site-packages/Martel/Generate.pyc
-lib/python${MODPY_VERSION}/site-packages/Martel/IterParser.py
-lib/python${MODPY_VERSION}/site-packages/Martel/IterParser.pyc
-lib/python${MODPY_VERSION}/site-packages/Martel/Iterator.py
-lib/python${MODPY_VERSION}/site-packages/Martel/Iterator.pyc
-lib/python${MODPY_VERSION}/site-packages/Martel/LAX.py
-lib/python${MODPY_VERSION}/site-packages/Martel/LAX.pyc
-lib/python${MODPY_VERSION}/site-packages/Martel/Parser.py
-lib/python${MODPY_VERSION}/site-packages/Martel/Parser.pyc
-lib/python${MODPY_VERSION}/site-packages/Martel/RecordReader.py
-lib/python${MODPY_VERSION}/site-packages/Martel/RecordReader.pyc
-lib/python${MODPY_VERSION}/site-packages/Martel/Time.py
-lib/python${MODPY_VERSION}/site-packages/Martel/Time.pyc
-lib/python${MODPY_VERSION}/site-packages/Martel/__init__.py
-lib/python${MODPY_VERSION}/site-packages/Martel/__init__.pyc
-lib/python${MODPY_VERSION}/site-packages/Martel/convert_re.py
-lib/python${MODPY_VERSION}/site-packages/Martel/convert_re.pyc
-lib/python${MODPY_VERSION}/site-packages/Martel/msre_constants.py
-lib/python${MODPY_VERSION}/site-packages/Martel/msre_constants.pyc
-lib/python${MODPY_VERSION}/site-packages/Martel/msre_parse.py
-lib/python${MODPY_VERSION}/site-packages/Martel/msre_parse.pyc
-lib/python${MODPY_VERSION}/site-packages/Martel/optimize.py
-lib/python${MODPY_VERSION}/site-packages/Martel/optimize.pyc
-@comment lib/python${MODPY_VERSION}/site-packages/Martel/setup.py
-@comment lib/python${MODPY_VERSION}/site-packages/Martel/setup.pyc
 lib/python${MODPY_VERSION}/site-packages/biopython-${MODPY_EGG_VERSION}-py${MODPY_VERSION}.egg-info
-share/doc/py-biopython/
-share/doc/py-biopython/Crystal.txt
-share/doc/py-biopython/FilteredReader.txt
-share/doc/py-biopython/NetCatch.txt
-share/doc/py-biopython/References.txt
-share/doc/py-biopython/Tutorial.txt
-share/examples/py-biopython/
-share/examples/py-biopython/clustal_run.py
-share/examples/py-biopython/fasta_dictionary.py
-share/examples/py-biopython/fasta_iterator.py
-share/examples/py-biopython/getgene.py
-share/examples/py-biopython/local_blast.py
-share/examples/py-biopython/ls_orchid.fasta
-share/examples/py-biopython/m_cold.fasta
-share/examples/py-biopython/make_subsmat.py
-share/examples/py-biopython/nmr/
-share/examples/py-biopython/nmr/noed.xpk
-share/examples/py-biopython/nmr/simplepredict.py
-share/examples/py-biopython/opuntia.fasta
-share/examples/py-biopython/protein.aln
-share/examples/py-biopython/pubmed_search.py
-share/examples/py-biopython/query_entrez.py
-share/examples/py-biopython/swissprot.py
-share/examples/py-biopython/www_blast.py
+share/doc/${MODPY_PY_PREFIX}biopython/
+share/doc/${MODPY_PY_PREFIX}biopython/Crystal.txt
+share/doc/${MODPY_PY_PREFIX}biopython/FilteredReader.txt
+share/doc/${MODPY_PY_PREFIX}biopython/NetCatch.txt
+share/doc/${MODPY_PY_PREFIX}biopython/References.txt
+share/doc/${MODPY_PY_PREFIX}biopython/Tutorial.txt
+share/examples/${MODPY_PY_PREFIX}biopython/
+share/examples/${MODPY_PY_PREFIX}biopython/ACT_example.py
+share/examples/${MODPY_PY_PREFIX}biopython/PF05371_seed.sth
+share/examples/${MODPY_PY_PREFIX}biopython/Proux_et_al_2002_Figure_6.py
+share/examples/${MODPY_PY_PREFIX}biopython/clustal_run.py
+share/examples/${MODPY_PY_PREFIX}biopython/fasta_dictionary.py
+share/examples/${MODPY_PY_PREFIX}biopython/fasta_iterator.py
+share/examples/${MODPY_PY_PREFIX}biopython/getgene.py
+share/examples/${MODPY_PY_PREFIX}biopython/local_blast.py
+share/examples/${MODPY_PY_PREFIX}biopython/ls_orchid.fasta
+share/examples/${MODPY_PY_PREFIX}biopython/ls_orchid.gbk
+share/examples/${MODPY_PY_PREFIX}biopython/ls_orchid.gbk.bgz
+share/examples/${MODPY_PY_PREFIX}biopython/m_cold.fasta
+share/examples/${MODPY_PY_PREFIX}biopython/make_subsmat.py
+share/examples/${MODPY_PY_PREFIX}biopython/nmr/
+share/examples/${MODPY_PY_PREFIX}biopython/nmr/noed.xpk
+share/examples/${MODPY_PY_PREFIX}biopython/nmr/simplepredict.py
+share/examples/${MODPY_PY_PREFIX}biopython/opuntia.fasta
+share/examples/${MODPY_PY_PREFIX}biopython/protein.aln
+share/examples/${MODPY_PY_PREFIX}biopython/swissprot.py
+share/examples/${MODPY_PY_PREFIX}biopython/www_blast.py

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