- Update to 1.54

PR:		ports/148274
Submitted by:	Ju Pengfei <jupengfei@gmail.com>
Approved by:	maintainer
Feature safe:	yes

3 files changed, 146 insertions, 49 deletions

diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile
index d1598b9635e4..af35a6c59483 100644
--- a/biology/py-biopython/Makefile
+++ b/biology/py-biopython/Makefile
@@ -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 @@ PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 MAINTAINER=	mauricio@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 --git a/biology/py-biopython/distinfo b/biology/py-biopython/distinfo
index 5dbf46120d05..f6f417b05717 100644
--- a/biology/py-biopython/distinfo
+++ b/biology/py-biopython/distinfo
@@ -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 --git a/biology/py-biopython/pkg-plist b/biology/py-biopython/pkg-plist
index 3458048bde3a..afc36f563493 100644
--- a/biology/py-biopython/pkg-plist
+++ b/biology/py-biopython/pkg-plist
@@ -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
-@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
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+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmcommon_011101.dtd
 %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmcommon_080101.dtd
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+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedline_011101.dtd
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-%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd
+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd
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+%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd
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 %%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
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@@ -864,6 +939,12 @@
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 %%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
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@@ -897,15 +978,15 @@
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 %%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
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@@ -939,12 +1020,12 @@
 %%PYTHON_SITELIBDIR%%/Bio/Translate.py
 %%PYTHON_SITELIBDIR%%/Bio/Translate.pyc
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-%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.py
-%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyc
-%%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyo
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 %%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
+@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
+@dirrm %%PYTHON_SITELIBDIR%%/BioSQL