ports/148274: [update] biology/py-biopython
Ju Pengfei
jupengfei at gmail.com
Thu Jul 1 07:50:05 UTC 2010
>Number: 148274
>Category: ports
>Synopsis: [update] biology/py-biopython
>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 Jul 01 07:50:04 UTC 2010
>Closed-Date:
>Last-Modified:
>Originator: Ju Pengfei
>Release: 8.0-RELEASE-p3
>Organization:
Ju Pengfei
>Environment:
>Description:
update to 1.54.
Changes:
removed lang/py-mx-base from BUILD_DEPENDS;
lang/py-mx-base is no longer used at all.
(ref: http://biopython.org/DIST/docs/install/Installation.html#htoc17)
>How-To-Repeat:
>Fix:
apply this patch, please.
thanks.
Patch attached with submission follows:
diff -ruN py-biopython.bak/Makefile py-biopython/Makefile
--- py-biopython.bak/Makefile 2010-01-06 08:29:25.000000000 +0800
+++ py-biopython/Makefile 2010-07-01 15:13:26.000000000 +0800
@@ -6,7 +6,7 @@
#
PORTNAME= biopython
-PORTVERSION= 1.53
+PORTVERSION= 1.54
CATEGORIES= biology python
MASTER_SITES= http://www.biopython.org/DIST/
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -14,8 +14,7 @@
MAINTAINER= mauricio at arareko.net
COMMENT= A collection of Python modules for bioinformatics
-BUILD_DEPENDS= ${PYNUMPY} \
- ${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base
+BUILD_DEPENDS= ${PYNUMPY}
RUN_DEPENDS= ${BUILD_DEPENDS}
USE_PYTHON= 2.4+
diff -ruN py-biopython.bak/distinfo py-biopython/distinfo
--- py-biopython.bak/distinfo 2010-01-06 08:29:25.000000000 +0800
+++ py-biopython/distinfo 2010-07-01 10:38:07.000000000 +0800
@@ -1,3 +1,3 @@
-MD5 (biopython-1.53.tar.gz) = df1004ec64b9b593c0e690c14a20667a
-SHA256 (biopython-1.53.tar.gz) = 0db8bf8d37641fdfc6a8aac248de3d8cb4111e55484deb43f67e8d7ad082013f
-SIZE (biopython-1.53.tar.gz) = 4284683
+MD5 (biopython-1.54.tar.gz) = d4c4ce5a3e1bb401928ca3dc3d1b08cd
+SHA256 (biopython-1.54.tar.gz) = 6f704698d68af75b3601b2a862386682b2317038b8bbaf2eb2ad68c1e1a4dc35
+SIZE (biopython-1.54.tar.gz) = 6445527
diff -ruN py-biopython.bak/pkg-plist py-biopython/pkg-plist
--- py-biopython.bak/pkg-plist 2010-01-06 08:29:25.000000000 +0800
+++ py-biopython/pkg-plist 2010-07-01 15:25:17.000000000 +0800
@@ -1,19 +1,3 @@
-%%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
- at dirrm %%PYTHON_SITELIBDIR%%/BioSQL
%%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.py
%%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.pyc
%%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.pyo
@@ -189,6 +173,8 @@
%%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_BlastOutput.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd
@@ -219,29 +205,88 @@
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/PIR_General.mod.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/PRF_General.mod.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/SP_General.mod.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/XHTMLtablesetup.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/archivearticle.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/archivecustom-classes.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/archivecustom-mixes.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/archivecustom-models.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/archivecustom-modules.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/articlemeta.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/backmatter.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/chars.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/common.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/default-classes.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/default-mixes.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/display.ent
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eInfo_020511.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eLink_020511.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eLink_090910.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/ePost_020511.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eSearch_020511.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eSpell.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eSummary_041029.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/egquery.dtd
-%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pmc-1.dtd
-%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_100101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/elink_020122.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/format.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/htmltable.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isoamsa.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isoamsb.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isoamsc.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isoamsn.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isoamso.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isoamsr.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isobox.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isocyr1.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isocyr2.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isodia.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isogrk1.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isogrk2.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isogrk3.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isogrk4.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isolat1.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isolat2.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isomfrk.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isomopf.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isomscr.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isonum.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isopub.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/isotech.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/journalmeta.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/link.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/list.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/math.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/mathml2-qname-1.mod
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/mathml2.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/mathmlsetup.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/mmlalias.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/mmlextra.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/modules.ent
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmcommon_011101.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmcommon_080101.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmcommon_090101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedline_011101.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedline_080101.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedline_090101.dtd
-%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.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/notat.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/para.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/phrase.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pmc-1.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_020114.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_080101.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_090101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_100101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/references.ent
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/section.ent
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/taxon.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/xmlspecchars.ent
%%PYTHON_SITELIBDIR%%/Bio/Entrez/Parser.py
%%PYTHON_SITELIBDIR%%/Bio/Entrez/Parser.pyc
%%PYTHON_SITELIBDIR%%/Bio/Entrez/Parser.pyo
@@ -498,12 +543,12 @@
%%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/MAST.py
%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MAST.pyc
%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MAST.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
@@ -692,6 +737,36 @@
%%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/BaseTree.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/BaseTree.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/BaseTree.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/Newick.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/Newick.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/Newick.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/NewickIO.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/NewickIO.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/NewickIO.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/NexusIO.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/NexusIO.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/NexusIO.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXML.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXML.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXML.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXMLIO.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXMLIO.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/PhyloXMLIO.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_io.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_io.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_io.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_sugar.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_sugar.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_sugar.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_utils.py
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_utils.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Phylo/_utils.pyo
%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.py
%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.pyc
%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.pyo
@@ -710,15 +785,18 @@
%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.py
-%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyc
-%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyo
%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Controller.py
%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Controller.pyc
%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Controller.pyo
%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/EasyController.py
%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/EasyController.pyc
%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/EasyController.pyo
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/FileParser.py
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/FileParser.pyc
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/FileParser.pyo
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.py
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyc
+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyo
%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.pyo
@@ -789,9 +867,6 @@
%%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.py
%%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.pyc
%%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.pyo
@@ -810,6 +885,9 @@
%%PYTHON_SITELIBDIR%%/Bio/SCOP/Residues.py
%%PYTHON_SITELIBDIR%%/Bio/SCOP/Residues.pyc
%%PYTHON_SITELIBDIR%%/Bio/SCOP/Residues.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.py
%%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.pyc
%%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.pyo
@@ -825,12 +903,6 @@
%%PYTHON_SITELIBDIR%%/Bio/SeqFeature.py
%%PYTHON_SITELIBDIR%%/Bio/SeqFeature.pyc
%%PYTHON_SITELIBDIR%%/Bio/SeqFeature.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.py
-%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.pyo
-%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.py
-%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.pyc
-%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.pyo
%%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.py
%%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.pyc
%%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.pyo
@@ -855,6 +927,9 @@
%%PYTHON_SITELIBDIR%%/Bio/SeqIO/QualityIO.py
%%PYTHON_SITELIBDIR%%/Bio/SeqIO/QualityIO.pyc
%%PYTHON_SITELIBDIR%%/Bio/SeqIO/QualityIO.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SffIO.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SffIO.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SffIO.pyo
%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.py
%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.pyc
%%PYTHON_SITELIBDIR%%/Bio/SeqIO/SwissIO.pyo
@@ -864,6 +939,12 @@
%%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/SeqIO/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.pyo
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.py
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.pyc
+%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.pyo
%%PYTHON_SITELIBDIR%%/Bio/SeqRecord.py
%%PYTHON_SITELIBDIR%%/Bio/SeqRecord.pyc
%%PYTHON_SITELIBDIR%%/Bio/SeqRecord.pyo
@@ -897,15 +978,15 @@
%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.py
%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.pyc
%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.py
-%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyo
-%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/_Novoalign.py
%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/_Novoalign.pyc
%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/_Novoalign.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.pyo
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.py
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyc
+%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyo
%%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.pyo
@@ -939,12 +1020,12 @@
%%PYTHON_SITELIBDIR%%/Bio/Translate.py
%%PYTHON_SITELIBDIR%%/Bio/Translate.pyc
%%PYTHON_SITELIBDIR%%/Bio/Translate.pyo
-%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.py
%%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.pyc
%%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.pyo
+%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.py
+%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyc
+%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.pyo
@@ -981,6 +1062,21 @@
%%PYTHON_SITELIBDIR%%/Bio/utils.py
%%PYTHON_SITELIBDIR%%/Bio/utils.pyc
%%PYTHON_SITELIBDIR%%/Bio/utils.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
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Affy
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Align/Applications
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Align
@@ -1035,6 +1131,7 @@
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Parsers
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway/Rep
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway
+ at dirrm %%PYTHON_SITELIBDIR%%/Bio/Phylo
@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async
@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist
@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop
@@ -1056,3 +1153,4 @@
@dirrm %%PYTHON_SITELIBDIR%%/Bio/UniGene
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Wise
@dirrm %%PYTHON_SITELIBDIR%%/Bio
+ at dirrm %%PYTHON_SITELIBDIR%%/BioSQL
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>Audit-Trail:
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