From owner-freebsd-ports-bugs@FreeBSD.ORG Thu Apr 23 14:40:01 2009 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 155C21065672 for ; Thu, 23 Apr 2009 14:40:01 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id E254F8FC1F for ; Thu, 23 Apr 2009 14:40:00 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.14.3/8.14.3) with ESMTP id n3NEe0uC084495 for ; Thu, 23 Apr 2009 14:40:00 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.3/8.14.3/Submit) id n3NEe0gl084494; Thu, 23 Apr 2009 14:40:00 GMT (envelope-from gnats) Resent-Date: Thu, 23 Apr 2009 14:40:00 GMT Resent-Message-Id: <200904231440.n3NEe0gl084494@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Wen heping Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 849BD1065672 for ; Thu, 23 Apr 2009 14:37:59 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (www.freebsd.org [IPv6:2001:4f8:fff6::21]) by mx1.freebsd.org (Postfix) with ESMTP id 70FB98FC12 for ; Thu, 23 Apr 2009 14:37:59 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (localhost [127.0.0.1]) by www.freebsd.org (8.14.3/8.14.3) with ESMTP id n3NEbx5h021920 for ; Thu, 23 Apr 2009 14:37:59 GMT (envelope-from nobody@www.freebsd.org) Received: (from nobody@localhost) by www.freebsd.org (8.14.3/8.14.3/Submit) id n3NEbxXv021918; Thu, 23 Apr 2009 14:37:59 GMT (envelope-from nobody) Message-Id: <200904231437.n3NEbxXv021918@www.freebsd.org> Date: Thu, 23 Apr 2009 14:37:59 GMT From: Wen heping To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-3.1 Cc: Subject: ports/133951: [Update]biology/py-biopython:update to 1.50 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 23 Apr 2009 14:40:01 -0000 >Number: 133951 >Category: ports >Synopsis: [Update]biology/py-biopython:update to 1.50 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Thu Apr 23 14:40:00 UTC 2009 >Closed-Date: >Last-Modified: >Originator: Wen heping >Release: FreeBSD 8.0-CURRENT >Organization: ChangAn Middle School >Environment: FreeBSD fb8.wenjing.com 8.0-CURRENT FreeBSD 8.0-CURRENT #0: Sun Mar 22 22:12:06 CST 2009 root@fb8.wenjing.com:/usr/obj/usr/src/sys/GENERIC i386 >Description: update to 1.50 from 1.48 >How-To-Repeat: >Fix: Patch attached with submission follows: diff -u py-biopython/Makefile py-biopython.new/Makefile --- py-biopython/Makefile 2009-04-23 11:43:44.000000000 +0800 +++ py-biopython.new/Makefile 2009-04-23 22:14:25.000000000 +0800 @@ -6,7 +6,7 @@ # PORTNAME= biopython -PORTVERSION= 1.48 +PORTVERSION= 1.50 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/DIST/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -14,13 +14,13 @@ 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 -u py-biopython/distinfo py-biopython.new/distinfo --- py-biopython/distinfo 2009-04-23 11:43:44.000000000 +0800 +++ py-biopython.new/distinfo 2009-04-23 11:44:11.000000000 +0800 @@ -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-1.50.tar.gz) = 3b29187846baa223c7c1a4e9a058e6b9 +SHA256 (biopython-1.50.tar.gz) = 7a4d32a83841159e912c7914b35fb4e17cdcf447ae8266fe5b31b5a3a495d783 +SIZE (biopython-1.50.tar.gz) = 4660143 Only in py-biopython: files diff -u py-biopython/pkg-plist py-biopython.new/pkg-plist --- py-biopython/pkg-plist 2009-04-23 11:43:44.000000000 +0800 +++ py-biopython.new/pkg-plist 2009-04-23 22:31:05.000000000 +0800 @@ -1,12 +1,25 @@ +%%PYTHON_SITELIBDIR%%/BioSQL/__init__.py +%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyc +%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyo +%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.py +%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyc +%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.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/Loader.py +%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyc +%%PYTHON_SITELIBDIR%%/BioSQL/Loader.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 @@ -100,15 +113,6 @@ %%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 @@ -140,15 +144,6 @@ %%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 @@ -248,11 +243,10 @@ %%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 +287,41 @@ %%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 +433,6 @@ %%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 +445,39 @@ %%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 @@ -469,9 +514,6 @@ %%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 -%%PYTHON_SITELIBDIR%%/Bio/LocusLink/web_parse.pyc -%%PYTHON_SITELIBDIR%%/Bio/LocusLink/web_parse.pyo %%PYTHON_SITELIBDIR%%/Bio/LogisticRegression.py %%PYTHON_SITELIBDIR%%/Bio/LogisticRegression.pyc %%PYTHON_SITELIBDIR%%/Bio/LogisticRegression.pyo @@ -557,6 +590,24 @@ %%PYTHON_SITELIBDIR%%/Bio/Mindy/compression.py %%PYTHON_SITELIBDIR%%/Bio/Mindy/compression.pyc %%PYTHON_SITELIBDIR%%/Bio/Mindy/compression.pyo +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/AlignAce.py +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/AlignAce.pyc +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/AlignAce.pyo +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.py +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.pyc +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.pyo +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/Motif/Thresholds.py +%%PYTHON_SITELIBDIR%%/Bio/Motif/Thresholds.pyc +%%PYTHON_SITELIBDIR%%/Bio/Motif/Thresholds.pyo +%%PYTHON_SITELIBDIR%%/Bio/Motif/_Motif.py +%%PYTHON_SITELIBDIR%%/Bio/Motif/_Motif.pyc +%%PYTHON_SITELIBDIR%%/Bio/Motif/_Motif.pyo +%%PYTHON_SITELIBDIR%%/Bio/Motif/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/Motif/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/Motif/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/NBRF/Record.py %%PYTHON_SITELIBDIR%%/Bio/NBRF/Record.pyc %%PYTHON_SITELIBDIR%%/Bio/NBRF/Record.pyo @@ -747,9 +798,6 @@ %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.py %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.pyc %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.pyo @@ -799,6 +847,9 @@ %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/split_ssm_2d.par %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/ssm_1d.par %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/ssm_2d.par +%%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/PropertyManager.py %%PYTHON_SITELIBDIR%%/Bio/PropertyManager.pyc %%PYTHON_SITELIBDIR%%/Bio/PropertyManager.pyo @@ -814,9 +865,6 @@ %%PYTHON_SITELIBDIR%%/Bio/PubMed.py %%PYTHON_SITELIBDIR%%/Bio/PubMed.pyc %%PYTHON_SITELIBDIR%%/Bio/PubMed.pyo -%%PYTHON_SITELIBDIR%%/Bio/Rebase/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/Rebase/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/Rebase/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/Restriction/DNAUtils.so %%PYTHON_SITELIBDIR%%/Bio/Restriction/PrintFormat.py %%PYTHON_SITELIBDIR%%/Bio/Restriction/PrintFormat.pyc @@ -866,9 +914,6 @@ %%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.py %%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/SGMLExtractor.py -%%PYTHON_SITELIBDIR%%/Bio/SGMLExtractor.pyc -%%PYTHON_SITELIBDIR%%/Bio/SGMLExtractor.pyo %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.py %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.pyc %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.pyo @@ -896,9 +941,6 @@ %%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.py %%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.pyo -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/ClustalIO.py -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/ClustalIO.pyc -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/ClustalIO.pyo %%PYTHON_SITELIBDIR%%/Bio/SeqIO/FastaIO.py %%PYTHON_SITELIBDIR%%/Bio/SeqIO/FastaIO.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqIO/FastaIO.pyo @@ -911,21 +953,15 @@ %%PYTHON_SITELIBDIR%%/Bio/SeqIO/Interfaces.py %%PYTHON_SITELIBDIR%%/Bio/SeqIO/Interfaces.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqIO/Interfaces.pyo -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/NexusIO.py -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/NexusIO.pyc -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/NexusIO.pyo %%PYTHON_SITELIBDIR%%/Bio/SeqIO/PhdIO.py %%PYTHON_SITELIBDIR%%/Bio/SeqIO/PhdIO.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqIO/PhdIO.pyo -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/PhylipIO.py -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/PhylipIO.pyc -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/PhylipIO.pyo %%PYTHON_SITELIBDIR%%/Bio/SeqIO/PirIO.py %%PYTHON_SITELIBDIR%%/Bio/SeqIO/PirIO.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqIO/PirIO.pyo -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/StockholmIO.py -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/StockholmIO.pyc -%%PYTHON_SITELIBDIR%%/Bio/SeqIO/StockholmIO.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/QualityIO.py +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/QualityIO.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/QualityIO.pyo %%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.py %%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.pyo @@ -941,9 +977,6 @@ %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CheckSum.py %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CheckSum.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CheckSum.pyo -%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/lcc.py -%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/lcc.pyc -%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/lcc.pyo %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.py %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.pyo @@ -965,6 +998,9 @@ %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/__init__.py %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/lcc.py +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/lcc.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/lcc.pyo %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.py %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.pyc %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.pyo @@ -1031,153 +1067,14 @@ %%PYTHON_SITELIBDIR%%/Bio/__init__.py %%PYTHON_SITELIBDIR%%/Bio/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/builders/Search/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/builders/Search/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/builders/Search/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/builders/Search/search.py -%%PYTHON_SITELIBDIR%%/Bio/builders/Search/search.pyc -%%PYTHON_SITELIBDIR%%/Bio/builders/Search/search.pyo -%%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord/sequence.py -%%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord/sequence.pyc -%%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord/sequence.pyo -%%PYTHON_SITELIBDIR%%/Bio/builders/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/builders/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/builders/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/cMarkovModel.so -%%PYTHON_SITELIBDIR%%/Bio/cdistance.so %%PYTHON_SITELIBDIR%%/Bio/clistfns.so %%PYTHON_SITELIBDIR%%/Bio/cmathfns.so -%%PYTHON_SITELIBDIR%%/Bio/config/DBRegistry.py -%%PYTHON_SITELIBDIR%%/Bio/config/DBRegistry.pyc -%%PYTHON_SITELIBDIR%%/Bio/config/DBRegistry.pyo -%%PYTHON_SITELIBDIR%%/Bio/config/FormatRegistry.py -%%PYTHON_SITELIBDIR%%/Bio/config/FormatRegistry.pyc -%%PYTHON_SITELIBDIR%%/Bio/config/FormatRegistry.pyo -%%PYTHON_SITELIBDIR%%/Bio/config/Registry.py -%%PYTHON_SITELIBDIR%%/Bio/config/Registry.pyc -%%PYTHON_SITELIBDIR%%/Bio/config/Registry.pyo -%%PYTHON_SITELIBDIR%%/Bio/config/SeqDBRegistry.py -%%PYTHON_SITELIBDIR%%/Bio/config/SeqDBRegistry.pyc -%%PYTHON_SITELIBDIR%%/Bio/config/SeqDBRegistry.pyo -%%PYTHON_SITELIBDIR%%/Bio/config/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/config/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/config/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/config/_stanzaformat.py -%%PYTHON_SITELIBDIR%%/Bio/config/_stanzaformat.pyc -%%PYTHON_SITELIBDIR%%/Bio/config/_stanzaformat.pyo -%%PYTHON_SITELIBDIR%%/Bio/config/_support.py -%%PYTHON_SITELIBDIR%%/Bio/config/_support.pyc -%%PYTHON_SITELIBDIR%%/Bio/config/_support.pyo %%PYTHON_SITELIBDIR%%/Bio/cpairwise2.so %%PYTHON_SITELIBDIR%%/Bio/cstringfns.so -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/_support.py -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/_support.pyc -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/_support.pyo -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/embl.py -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/embl.pyc -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/embl.pyo -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/fasta.py -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/fasta.pyc -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/fasta.pyo -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/genbank.py -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/genbank.pyc -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/genbank.pyo -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/interpro.py -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/interpro.pyc -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/interpro.pyo -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/medline.py -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/medline.pyc -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/medline.pyo -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/pdb.py -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/pdb.pyc -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/pdb.pyo -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/prodoc.py -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/prodoc.pyc -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/prodoc.pyo -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/prosite.py -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/prosite.pyc -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/prosite.pyo -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/swissprot.py -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/swissprot.pyc -%%PYTHON_SITELIBDIR%%/Bio/dbdefs/swissprot.pyo %%PYTHON_SITELIBDIR%%/Bio/distance.py %%PYTHON_SITELIBDIR%%/Bio/distance.pyc %%PYTHON_SITELIBDIR%%/Bio/distance.pyo -%%PYTHON_SITELIBDIR%%/Bio/expressions/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/expressions/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/expressions/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/expressions/blast/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/expressions/blast/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/expressions/blast/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/expressions/blast/ncbiblast.py -%%PYTHON_SITELIBDIR%%/Bio/expressions/blast/ncbiblast.pyc -%%PYTHON_SITELIBDIR%%/Bio/expressions/blast/ncbiblast.pyo -%%PYTHON_SITELIBDIR%%/Bio/expressions/blast/wublast.py -%%PYTHON_SITELIBDIR%%/Bio/expressions/blast/wublast.pyc -%%PYTHON_SITELIBDIR%%/Bio/expressions/blast/wublast.pyo -%%PYTHON_SITELIBDIR%%/Bio/expressions/blocks.py -%%PYTHON_SITELIBDIR%%/Bio/expressions/blocks.pyc -%%PYTHON_SITELIBDIR%%/Bio/expressions/blocks.pyo -%%PYTHON_SITELIBDIR%%/Bio/expressions/embl/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/expressions/embl/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/expressions/embl/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/expressions/embl/embl65.py -%%PYTHON_SITELIBDIR%%/Bio/expressions/embl/embl65.pyc -%%PYTHON_SITELIBDIR%%/Bio/expressions/embl/embl65.pyo -%%PYTHON_SITELIBDIR%%/Bio/expressions/fasta.py -%%PYTHON_SITELIBDIR%%/Bio/expressions/fasta.pyc -%%PYTHON_SITELIBDIR%%/Bio/expressions/fasta.pyo -%%PYTHON_SITELIBDIR%%/Bio/expressions/genbank.py -%%PYTHON_SITELIBDIR%%/Bio/expressions/genbank.pyc -%%PYTHON_SITELIBDIR%%/Bio/expressions/genbank.pyo -%%PYTHON_SITELIBDIR%%/Bio/expressions/hmmpfam.py -%%PYTHON_SITELIBDIR%%/Bio/expressions/hmmpfam.pyc -%%PYTHON_SITELIBDIR%%/Bio/expressions/hmmpfam.pyo -%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/ipi.py -%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/ipi.pyc -%%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 @@ -1215,68 +1112,7 @@ %%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 @dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignAce @dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignIO @@ -1284,20 +1120,19 @@ @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 @@ -1308,7 +1143,7 @@ @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 @@ -1318,11 +1153,12 @@ @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/Motif/Parsers +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Motif @dirrm %%PYTHON_SITELIBDIR%%/Bio/NBRF @dirrm %%PYTHON_SITELIBDIR%%/Bio/NMR @dirrm %%PYTHON_SITELIBDIR%%/Bio/Ndb @@ -1330,19 +1166,18 @@ @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 @@ -1357,18 +1192,52 @@ @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 +%%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%%/Martel >Release-Note: >Audit-Trail: >Unformatted: