ports/133951: [Update]biology/py-biopython:update to 1.50
Wen heping
wenheping at gmail.com
Thu Apr 23 14:40:01 UTC 2009
>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 at 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 at 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
+ at 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
- at 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
- at 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
- at 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
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Entrez
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Enzyme
+ at 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
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/Gobase
+ at 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
- at 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
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers
+ at 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
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async
- at 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
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Prosite
- at 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
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/Search
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/builders
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/config
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/dbdefs
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/blast
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/embl
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions
- at dirrm %%PYTHON_SITELIBDIR%%/Bio/formatdefs
@dirrm %%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord
@dirrm %%PYTHON_SITELIBDIR%%/Bio/writers
@dirrm %%PYTHON_SITELIBDIR%%/Bio
- at 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:
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