Attachment 107469 Details for Bug 148274 – file.diff

[patch] file.diff

file.diff (text/plain), 16.75 KB, created by Ju Pengfei on 2010-07-01 08:50:04 UTC

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Description:

Filename:

MIME Type:

Creator: Ju Pengfei

Created: 2010-07-01 08:50:04 UTC

Size: 16.75 KB

patch

obsolete

>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@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
>-@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
>+@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

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Attachments on bug 148274: 107469