On Thu, Aug 20, 2020 at 12:20:32PM +0200, Charlene Wendling wrote: > Hi, > > Our current bioperl related ports are old, and we had to patch > them already to deal with Perl changes. So i'm proposing an update here > to 1.7.7 to avoid dealing with emergency fixes at a large scale. > > These updates and new ports will not totally replace what bioperl used > to provide, see [0] for an exhaustive list of what it implies. > > There are backward incompatibilities, and a lot of inter dependencies, > so you need all these ports at once, since bioperl has been split in > many modules. This also means that conflict markers had to be sprinkled > around, as hinted by update-plist(1). > > Updates are in the diff below, new ports are attached. > > biology/bioperl => PASS > biology/p5-Bio-ASN1-EntrezGene => PASS > biology/p5-Bio-Cluster => NEW, PASS > biology/p5-Bio-Variation => NEW, PASS > biology/p5-Bio-DB-NCBIHelper => NEW, PASS, NETWORK > biology/p5-Bio-DB-EMBL => NEW, PASS, NETWORK > > (NETWORK ones requires network for testing if you use PORTS_PRIVSEP) > > There are no other ports depending on bioperl. > > Comments/feedback are welcome,
OK afresh1@ not sure if there's something to be done about the network tests, but it did throw me off for a minute. > > Charlène. > > > [0] https://metacpan.org/changes/distribution/BioPerl#L71 > > > Index: bioperl/Makefile > =================================================================== > RCS file: /cvs/ports/biology/bioperl/Makefile,v > retrieving revision 1.21 > diff -u -p -r1.21 Makefile > --- bioperl/Makefile 12 Jul 2019 20:43:43 -0000 1.21 > +++ bioperl/Makefile 20 Aug 2020 10:11:28 -0000 > @@ -2,68 +2,51 @@ > > COMMENT= perl tools for bioinformatics > > -DISTNAME= BioPerl-1.6.924 > -REVISION= 1 > +DISTNAME= BioPerl-1.7.7 > PKGNAME= ${DISTNAME:L}# No p5-prefix here. > CATEGORIES= biology > > HOMEPAGE= https://bioperl.org/ > > -# perl > +# Perl > PERMIT_PACKAGE= Yes > > -CPAN_AUTHOR= CJFIELDS > - > MODULES= cpan > -PKG_ARCH= * > + > +CPAN_AUTHOR= CJFIELDS > MODCPAN_EXAMPLES= Yes > MODCPAN_EXAMPLES_DIR= ${PREFIX}/share/examples/bioperl/ > > -CONFIGURE_STYLE= modbuild > +RUN_DEPENDS= devel/p5-Data-Stag \ > + devel/p5-Error \ > + devel/p5-Graph \ > + devel/p5-IO-String \ > + devel/p5-IO-stringy \ > + devel/p5-IPC-Run \ > + devel/p5-List-MoreUtils \ > + devel/p5-Module-Build \ > + devel/p5-Set-Scalar \ > + devel/p5-Test-Most \ > + devel/p5-Test-RequiresInternet \ > + devel/p5-YAML \ > + textproc/p5-Libxml \ > + textproc/p5-XML-DOM \ > + textproc/p5-XML-DOM-XPath \ > + textproc/p5-XML-LibXML \ > + textproc/p5-XML-SAX \ > + textproc/p5-XML-SAX-Base \ > + textproc/p5-XML-SAX-Writer \ > + textproc/p5-XML-Twig \ > + textproc/p5-XML-Writer \ > + www/p5-HTTP-Message \ > + www/p5-URI \ > + www/p5-libwww > +TEST_DEPENDS= devel/p5-Test-Memory-Cycle \ > + devel/p5-Test-Weaken > > -BUILD_DEPENDS= ${RUN_DEPENDS} > -RUN_DEPENDS= biology/AcePerl \ > - databases/p5-DBD-mysql \ > - converters/p5-Convert-Binary-C \ > - devel/p5-Algorithm-Munkres \ > - devel/p5-Array-Compare \ > - devel/p5-Class-AutoClass \ > - devel/p5-Clone \ > - devel/p5-Data-Stag \ > - devel/p5-Graph \ > - devel/p5-IO-String \ > - devel/p5-IO-stringy \ > - devel/p5-Set-Scalar \ > - devel/p5-Test-Exception \ > - devel/p5-Tree-DAG_Node \ > - graphics/p5-GD \ > - graphics/p5-GD-SVG \ > - graphics/p5-SVG-Graph \ > - math/p5-GraphViz \ > - misc/p5-Spreadsheet-ParseExcel \ > - misc/p5-Spreadsheet-WriteExcel \ > - textproc/p5-XML-DOM \ > - textproc/p5-Libxml \ > - textproc/p5-XML-DOM-XPath \ > - textproc/p5-XML-Parser \ > - textproc/p5-XML-SAX-Writer \ > - textproc/p5-XML-Simple \ > - textproc/p5-XML-Twig \ > - textproc/p5-XML-Writer \ > - www/p5-CGI \ > - www/p5-HTML-Parser \ > - www/p5-SOAP-Lite \ > - www/p5-URI \ > - www/p5-libwww > -TEST_DEPENDS= devel/p5-Test-Most \ > - www/p5-HTML-TableExtract > - > -MAKE_ENV += TEST_POD=Yes > - > -# Optional (not ported) dependencies: > -# Postscript-TextBlock > -# Tie-Cacher > > -CONFIGURE_ENV+= PERL_MM_USE_DEFAULT=Yes > +MAKE_ENV += TEST_POD=Yes > + > +PKG_ARCH= * > > .include <bsd.port.mk> > Index: bioperl/distinfo > =================================================================== > RCS file: /cvs/ports/biology/bioperl/distinfo,v > retrieving revision 1.5 > diff -u -p -r1.5 distinfo > --- bioperl/distinfo 3 Apr 2015 09:46:53 -0000 1.5 > +++ bioperl/distinfo 20 Aug 2020 10:11:28 -0000 > @@ -1,2 +1,2 @@ > -SHA256 (BioPerl-1.6.924.tar.gz) = > YWp1Rrs8WFBN4nMEoPbLkE4YtrvNtqTshFTyvTe7dtA= > -SIZE (BioPerl-1.6.924.tar.gz) = 12623118 > +SHA256 (BioPerl-1.7.7.tar.gz) = cw4r04t1UL9rvVvKUNAZpwzKUUVZcCwTiddw/2nP8bs= > +SIZE (BioPerl-1.7.7.tar.gz) = 7532782 > Index: bioperl/patches/patch-Bio_Tools_Alignment_Consed_pm > =================================================================== > RCS file: bioperl/patches/patch-Bio_Tools_Alignment_Consed_pm > diff -N bioperl/patches/patch-Bio_Tools_Alignment_Consed_pm > --- bioperl/patches/patch-Bio_Tools_Alignment_Consed_pm 21 Feb 2019 > 10:25:48 -0000 1.1 > +++ /dev/null 1 Jan 1970 00:00:00 -0000 > @@ -1,15 +0,0 @@ > -$OpenBSD: patch-Bio_Tools_Alignment_Consed_pm,v 1.1 2019/02/21 10:25:48 cwen > Exp $ > -Fix: > -Error: Can't redeclare "my" in "my" > -Index: Bio/Tools/Alignment/Consed.pm > ---- Bio/Tools/Alignment/Consed.pm.orig > -+++ Bio/Tools/Alignment/Consed.pm > -@@ -1709,7 +1709,7 @@ Recursion is kewl, but this sub should likely be _reve > - > - > - sub reverse_recurse($$) { > -- my ($r_source,my $r_destination) = @_; > -+ my ($r_source, $r_destination) = @_; > - if (!@$r_source) { > - return $r_destination; > - } > Index: bioperl/patches/patch-Bio_Tools_SiRNA_Ruleset_tuschl_pm > =================================================================== > RCS file: bioperl/patches/patch-Bio_Tools_SiRNA_Ruleset_tuschl_pm > diff -N bioperl/patches/patch-Bio_Tools_SiRNA_Ruleset_tuschl_pm > --- bioperl/patches/patch-Bio_Tools_SiRNA_Ruleset_tuschl_pm 21 Feb 2019 > 10:25:48 -0000 1.1 > +++ /dev/null 1 Jan 1970 00:00:00 -0000 > @@ -1,16 +0,0 @@ > -$OpenBSD: patch-Bio_Tools_SiRNA_Ruleset_tuschl_pm,v 1.1 2019/02/21 10:25:48 > cwen Exp $ > -Avoid some of the super annoying warnings about deprecated braces > -Index: Bio/Tools/SiRNA/Ruleset/tuschl.pm > ---- Bio/Tools/SiRNA/Ruleset/tuschl.pm.orig > -+++ Bio/Tools/SiRNA/Ruleset/tuschl.pm > -@@ -178,8 +178,8 @@ sub _get_oligos { > - my $target = $2; > - > - # check for too many Gs (or Cs on the other strand) > -- next if ( $target =~ /G{ $self->gstring,}/io ); > -- next if ( $target =~ /C{ $self->gstring,}/io ); > -+ next if ( $target =~ /G\{ $self->gstring,\}/io ); > -+ next if ( $target =~ /C\{ $self->gstring,\}/io ); > - # skip Ns (for filtering) > - next if ( $target =~ /N/i); > - > Index: bioperl/patches/patch-maintenance_symlink_script_pl > =================================================================== > RCS file: bioperl/patches/patch-maintenance_symlink_script_pl > diff -N bioperl/patches/patch-maintenance_symlink_script_pl > --- bioperl/patches/patch-maintenance_symlink_script_pl 21 Feb 2019 > 10:25:48 -0000 1.2 > +++ /dev/null 1 Jan 1970 00:00:00 -0000 > @@ -1,15 +0,0 @@ > -$OpenBSD: patch-maintenance_symlink_script_pl,v 1.2 2019/02/21 10:25:48 cwen > Exp $ > -Index: maintenance/symlink_script.pl > ---- maintenance/symlink_script.pl.orig > -+++ maintenance/symlink_script.pl > -@@ -12,7 +12,9 @@ my %symlink_scripts = ('bp_bulk_load_gff.pl' => 'bp_pg > - # installation process installs the symlink as the actual file, so we may as > - # well have just done a copy > - > --my $install_dir = $build->install_destination('script'); > -+my $destdir = $build->runtime_params('destdir'); > -+my $install_dir = $destdir . $build->install_destination('script'); > -+ > - $build->log_info("Will try to install symlinks to $install_dir\n"); > - my $orig_dir = $build->cwd; > - chdir($install_dir); > Index: bioperl/pkg/PLIST > =================================================================== > RCS file: /cvs/ports/biology/bioperl/pkg/PLIST,v > retrieving revision 1.5 > diff -u -p -r1.5 PLIST > --- bioperl/pkg/PLIST 3 Apr 2015 09:46:53 -0000 1.5 > +++ bioperl/pkg/PLIST 20 Aug 2020 10:11:28 -0000 > @@ -1,75 +1,48 @@ > @comment $OpenBSD: PLIST,v 1.5 2015/04/03 09:46:53 jasper Exp $ > -bin/bp_aacomp.pl > -bin/bp_biofetch_genbank_proxy.pl > -bin/bp_bioflat_index.pl > -bin/bp_biogetseq.pl > -bin/bp_blast2tree.pl > -bin/bp_bulk_load_gff.pl > -bin/bp_chaos_plot.pl > -bin/bp_classify_hits_kingdom.pl > -bin/bp_composite_LD.pl > -bin/bp_das_server.pl > -bin/bp_dbsplit.pl > -bin/bp_download_query_genbank.pl > -bin/bp_extract_feature_seq.pl > -bin/bp_fast_load_gff.pl > -bin/bp_fastam9_to_table.pl > -bin/bp_fetch.pl > -bin/bp_filter_search.pl > -bin/bp_flanks.pl > -bin/bp_gccalc.pl > -bin/bp_genbank2gff.pl > -bin/bp_genbank2gff3.pl > -bin/bp_generate_histogram.pl > -bin/bp_heterogeneity_test.pl > -bin/bp_hivq.pl > -bin/bp_hmmer_to_table.pl > -bin/bp_index.pl > -bin/bp_load_gff.pl > -bin/bp_local_taxonomydb_query.pl > -bin/bp_make_mrna_protein.pl > -bin/bp_mask_by_search.pl > -bin/bp_meta_gff.pl > -bin/bp_mrtrans.pl > -bin/bp_mutate.pl > -bin/bp_netinstall.pl > -bin/bp_nexus2nh.pl > -bin/bp_nrdb.pl > -bin/bp_oligo_count.pl > -bin/bp_pairwise_kaks.pl > -bin/bp_parse_hmmsearch.pl > -bin/bp_process_gadfly.pl > -bin/bp_process_sgd.pl > -bin/bp_process_wormbase.pl > -bin/bp_query_entrez_taxa.pl > -bin/bp_remote_blast.pl > -bin/bp_revtrans-motif.pl > -bin/bp_search2BSML.pl > -bin/bp_search2alnblocks.pl > -bin/bp_search2gff.pl > -bin/bp_search2table.pl > -bin/bp_search2tribe.pl > -bin/bp_seq_length.pl > -bin/bp_seqconvert.pl > -bin/bp_seqcut.pl > -bin/bp_seqfeature_delete.pl > -bin/bp_seqfeature_gff3.pl > -bin/bp_seqfeature_load.pl > -bin/bp_seqpart.pl > -bin/bp_seqret.pl > -bin/bp_seqretsplit.pl > -bin/bp_split_seq.pl > -bin/bp_sreformat.pl > -bin/bp_taxid4species.pl > -bin/bp_taxonomy2tree.pl > -bin/bp_translate_seq.pl > -bin/bp_tree2pag.pl > -bin/bp_unflatten_seq.pl > +bin/bp_aacomp > +bin/bp_bioflat_index > +bin/bp_biogetseq > +bin/bp_dbsplit > +bin/bp_extract_feature_seq > +bin/bp_fastam9_to_table > +bin/bp_fetch > +bin/bp_filter_search > +bin/bp_find-blast-matches > +bin/bp_gccalc > +bin/bp_genbank2gff3 > +bin/bp_index > +bin/bp_local_taxonomydb_query > +bin/bp_make_mrna_protein > +bin/bp_mask_by_search > +bin/bp_mrtrans > +bin/bp_mutate > +bin/bp_nexus2nh > +bin/bp_nrdb > +bin/bp_oligo_count > +bin/bp_process_gadfly > +bin/bp_process_sgd > +bin/bp_revtrans-motif > +bin/bp_search2alnblocks > +bin/bp_search2gff > +bin/bp_search2table > +bin/bp_search2tribe > +bin/bp_seq_length > +bin/bp_seqconvert > +bin/bp_seqcut > +bin/bp_seqpart > +bin/bp_seqret > +bin/bp_seqretsplit > +bin/bp_split_seq > +bin/bp_sreformat > +bin/bp_taxid4species > +bin/bp_taxonomy2tree > +bin/bp_translate_seq > +bin/bp_tree2pag > +bin/bp_unflatten_seq > ${P5SITE}/Bio/ > ${P5SITE}/Bio/Align/ > ${P5SITE}/Bio/Align/AlignI.pm > ${P5SITE}/Bio/Align/DNAStatistics.pm > -${P5SITE}/Bio/Align/Graphics.pm > ${P5SITE}/Bio/Align/PairwiseStatistics.pm > ${P5SITE}/Bio/Align/ProteinStatistics.pm > ${P5SITE}/Bio/Align/StatisticsI.pm > @@ -90,7 +63,6 @@ ${P5SITE}/Bio/AlignIO/mega.pm > ${P5SITE}/Bio/AlignIO/meme.pm > ${P5SITE}/Bio/AlignIO/metafasta.pm > ${P5SITE}/Bio/AlignIO/msf.pm > -${P5SITE}/Bio/AlignIO/nexml.pm > ${P5SITE}/Bio/AlignIO/nexus.pm > ${P5SITE}/Bio/AlignIO/pfam.pm > ${P5SITE}/Bio/AlignIO/phylip.pm > @@ -99,7 +71,6 @@ ${P5SITE}/Bio/AlignIO/proda.pm > ${P5SITE}/Bio/AlignIO/prodom.pm > ${P5SITE}/Bio/AlignIO/psi.pm > ${P5SITE}/Bio/AlignIO/selex.pm > -${P5SITE}/Bio/AlignIO/stockholm.pm > ${P5SITE}/Bio/AlignIO/xmfa.pm > ${P5SITE}/Bio/AnalysisI.pm > ${P5SITE}/Bio/AnalysisParserI.pm > @@ -121,60 +92,11 @@ ${P5SITE}/Bio/Annotation/Tree.pm > ${P5SITE}/Bio/Annotation/TypeManager.pm > ${P5SITE}/Bio/AnnotationCollectionI.pm > ${P5SITE}/Bio/AnnotationI.pm > -${P5SITE}/Bio/Assembly/ > -${P5SITE}/Bio/Assembly/Contig.pm > -${P5SITE}/Bio/Assembly/ContigAnalysis.pm > -${P5SITE}/Bio/Assembly/IO/ > -${P5SITE}/Bio/Assembly/IO.pm > -${P5SITE}/Bio/Assembly/IO/ace.pm > -${P5SITE}/Bio/Assembly/IO/bowtie.pm > -${P5SITE}/Bio/Assembly/IO/maq.pm > -${P5SITE}/Bio/Assembly/IO/phrap.pm > -${P5SITE}/Bio/Assembly/IO/sam.pm > -${P5SITE}/Bio/Assembly/IO/tigr.pm > -${P5SITE}/Bio/Assembly/Scaffold.pm > -${P5SITE}/Bio/Assembly/ScaffoldI.pm > -${P5SITE}/Bio/Assembly/Singlet.pm > -${P5SITE}/Bio/Assembly/Tools/ > -${P5SITE}/Bio/Assembly/Tools/ContigSpectrum.pm > -${P5SITE}/Bio/Cluster/ > -${P5SITE}/Bio/Cluster/ClusterFactory.pm > -${P5SITE}/Bio/Cluster/FamilyI.pm > -${P5SITE}/Bio/Cluster/SequenceFamily.pm > -${P5SITE}/Bio/Cluster/UniGene.pm > -${P5SITE}/Bio/Cluster/UniGeneI.pm > -${P5SITE}/Bio/ClusterI.pm > -${P5SITE}/Bio/ClusterIO/ > -${P5SITE}/Bio/ClusterIO.pm > -${P5SITE}/Bio/ClusterIO/dbsnp.pm > -${P5SITE}/Bio/ClusterIO/unigene.pm > ${P5SITE}/Bio/CodonUsage/ > ${P5SITE}/Bio/CodonUsage/IO.pm > ${P5SITE}/Bio/CodonUsage/Table.pm > -${P5SITE}/Bio/Coordinate/ > -${P5SITE}/Bio/Coordinate/Chain.pm > -${P5SITE}/Bio/Coordinate/Collection.pm > -${P5SITE}/Bio/Coordinate/ExtrapolatingPair.pm > -${P5SITE}/Bio/Coordinate/GeneMapper.pm > -${P5SITE}/Bio/Coordinate/Graph.pm > -${P5SITE}/Bio/Coordinate/MapperI.pm > -${P5SITE}/Bio/Coordinate/Pair.pm > -${P5SITE}/Bio/Coordinate/Result/ > -${P5SITE}/Bio/Coordinate/Result.pm > -${P5SITE}/Bio/Coordinate/Result/Gap.pm > -${P5SITE}/Bio/Coordinate/Result/Match.pm > -${P5SITE}/Bio/Coordinate/ResultI.pm > -${P5SITE}/Bio/Coordinate/Utils.pm > ${P5SITE}/Bio/DB/ > -${P5SITE}/Bio/DB/Ace.pm > -${P5SITE}/Bio/DB/BioFetch.pm > -${P5SITE}/Bio/DB/CUTG.pm > ${P5SITE}/Bio/DB/DBFetch.pm > -${P5SITE}/Bio/DB/EMBL.pm > -${P5SITE}/Bio/DB/EntrezGene.pm > -${P5SITE}/Bio/DB/Expression/ > -${P5SITE}/Bio/DB/Expression.pm > -${P5SITE}/Bio/DB/Expression/geo.pm > ${P5SITE}/Bio/DB/Failover.pm > ${P5SITE}/Bio/DB/Fasta.pm > ${P5SITE}/Bio/DB/FileCache.pm > @@ -188,122 +110,27 @@ ${P5SITE}/Bio/DB/Flat/BDB/genbank.pm > ${P5SITE}/Bio/DB/Flat/BDB/swiss.pm > ${P5SITE}/Bio/DB/Flat/BinarySearch.pm > ${P5SITE}/Bio/DB/GFF/ > -${P5SITE}/Bio/DB/GFF.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/ > -${P5SITE}/Bio/DB/GFF/Adaptor/ace.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/berkeleydb/ > -${P5SITE}/Bio/DB/GFF/Adaptor/berkeleydb.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/biofetch.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/biofetch_oracle.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/dbi/ > -${P5SITE}/Bio/DB/GFF/Adaptor/dbi.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/dbi/iterator.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/dbi/mysql.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/dbi/oracle.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/dbi/oracleace.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/dbi/pg.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/memory/ > -${P5SITE}/Bio/DB/GFF/Adaptor/memory.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm > -${P5SITE}/Bio/DB/GFF/Adaptor/memory/iterator.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/ > -${P5SITE}/Bio/DB/GFF/Aggregator.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/alignment.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/clone.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/coding.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/gene.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/match.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/none.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/orf.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/processed_transcript.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/so_transcript.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/transcript.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/ucsc_acembly.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/ucsc_genscan.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/ucsc_refgene.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/ucsc_softberry.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm > -${P5SITE}/Bio/DB/GFF/Aggregator/ucsc_unigene.pm > -${P5SITE}/Bio/DB/GFF/Featname.pm > -${P5SITE}/Bio/DB/GFF/Feature.pm > -${P5SITE}/Bio/DB/GFF/Homol.pm > -${P5SITE}/Bio/DB/GFF/RelSegment.pm > -${P5SITE}/Bio/DB/GFF/Segment.pm > -${P5SITE}/Bio/DB/GFF/Typename.pm > ${P5SITE}/Bio/DB/GFF/Util/ > ${P5SITE}/Bio/DB/GFF/Util/Binning.pm > ${P5SITE}/Bio/DB/GFF/Util/Rearrange.pm > -${P5SITE}/Bio/DB/GenBank.pm > -${P5SITE}/Bio/DB/GenPept.pm > ${P5SITE}/Bio/DB/GenericWebAgent.pm > -${P5SITE}/Bio/DB/HIV/ > -${P5SITE}/Bio/DB/HIV.pm > -${P5SITE}/Bio/DB/HIV/HIVAnnotProcessor.pm > -${P5SITE}/Bio/DB/HIV/HIVQueryHelper.pm > -${P5SITE}/Bio/DB/HIV/lanl-schema.xml > ${P5SITE}/Bio/DB/InMemoryCache.pm > ${P5SITE}/Bio/DB/IndexedBase.pm > ${P5SITE}/Bio/DB/LocationI.pm > -${P5SITE}/Bio/DB/MeSH.pm > -${P5SITE}/Bio/DB/NCBIHelper.pm > ${P5SITE}/Bio/DB/Qual.pm > ${P5SITE}/Bio/DB/Query/ > -${P5SITE}/Bio/DB/Query/GenBank.pm > -${P5SITE}/Bio/DB/Query/HIVQuery.pm > ${P5SITE}/Bio/DB/Query/WebQuery.pm > ${P5SITE}/Bio/DB/QueryI.pm > ${P5SITE}/Bio/DB/RandomAccessI.pm > -${P5SITE}/Bio/DB/RefSeq.pm > ${P5SITE}/Bio/DB/ReferenceI.pm > ${P5SITE}/Bio/DB/Registry.pm > -${P5SITE}/Bio/DB/SeqFeature/ > -${P5SITE}/Bio/DB/SeqFeature.pm > -${P5SITE}/Bio/DB/SeqFeature/NormalizedFeature.pm > -${P5SITE}/Bio/DB/SeqFeature/NormalizedFeatureI.pm > -${P5SITE}/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm > -${P5SITE}/Bio/DB/SeqFeature/Segment.pm > -${P5SITE}/Bio/DB/SeqFeature/Store/ > -${P5SITE}/Bio/DB/SeqFeature/Store.pm > -${P5SITE}/Bio/DB/SeqFeature/Store/DBI/ > -${P5SITE}/Bio/DB/SeqFeature/Store/DBI/Iterator.pm > -${P5SITE}/Bio/DB/SeqFeature/Store/DBI/Pg.pm > -${P5SITE}/Bio/DB/SeqFeature/Store/DBI/SQLite.pm > -${P5SITE}/Bio/DB/SeqFeature/Store/DBI/mysql.pm > -${P5SITE}/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm > -${P5SITE}/Bio/DB/SeqFeature/Store/GFF2Loader.pm > -${P5SITE}/Bio/DB/SeqFeature/Store/GFF3Loader.pm > -${P5SITE}/Bio/DB/SeqFeature/Store/LoadHelper.pm > -${P5SITE}/Bio/DB/SeqFeature/Store/Loader.pm > -${P5SITE}/Bio/DB/SeqFeature/Store/bdb.pm > -${P5SITE}/Bio/DB/SeqFeature/Store/berkeleydb.pm > -${P5SITE}/Bio/DB/SeqFeature/Store/berkeleydb3.pm > -${P5SITE}/Bio/DB/SeqFeature/Store/memory.pm > -${P5SITE}/Bio/DB/SeqHound.pm > ${P5SITE}/Bio/DB/SeqI.pm > -${P5SITE}/Bio/DB/SeqVersion/ > -${P5SITE}/Bio/DB/SeqVersion.pm > -${P5SITE}/Bio/DB/SeqVersion/gi.pm > -${P5SITE}/Bio/DB/SwissProt.pm > -${P5SITE}/Bio/DB/TFBS/ > -${P5SITE}/Bio/DB/TFBS.pm > -${P5SITE}/Bio/DB/TFBS/transfac_pro.pm > ${P5SITE}/Bio/DB/Taxonomy/ > ${P5SITE}/Bio/DB/Taxonomy.pm > -${P5SITE}/Bio/DB/Taxonomy/entrez.pm > ${P5SITE}/Bio/DB/Taxonomy/flatfile.pm > ${P5SITE}/Bio/DB/Taxonomy/greengenes.pm > ${P5SITE}/Bio/DB/Taxonomy/list.pm > ${P5SITE}/Bio/DB/Taxonomy/silva.pm > -${P5SITE}/Bio/DB/Universal.pm > ${P5SITE}/Bio/DB/UpdateableSeqI.pm > ${P5SITE}/Bio/DB/WebDBSeqI.pm > ${P5SITE}/Bio/DBLinkContainerI.pm > @@ -312,8 +139,6 @@ ${P5SITE}/Bio/Das/FeatureTypeI.pm > ${P5SITE}/Bio/Das/SegmentI.pm > ${P5SITE}/Bio/DasI.pm > ${P5SITE}/Bio/DescribableI.pm > -${P5SITE}/Bio/Draw/ > -${P5SITE}/Bio/Draw/Pictogram.pm > ${P5SITE}/Bio/Event/ > ${P5SITE}/Bio/Event/EventGeneratorI.pm > ${P5SITE}/Bio/Event/EventHandlerI.pm > @@ -323,7 +148,6 @@ ${P5SITE}/Bio/Factory/ApplicationFactory > ${P5SITE}/Bio/Factory/DriverFactory.pm > ${P5SITE}/Bio/Factory/FTLocationFactory.pm > ${P5SITE}/Bio/Factory/LocationFactoryI.pm > -${P5SITE}/Bio/Factory/MapFactoryI.pm > ${P5SITE}/Bio/Factory/ObjectBuilderI.pm > ${P5SITE}/Bio/Factory/ObjectFactory.pm > ${P5SITE}/Bio/Factory/ObjectFactoryI.pm > @@ -346,31 +170,9 @@ ${P5SITE}/Bio/Index/EMBL.pm > ${P5SITE}/Bio/Index/Fasta.pm > ${P5SITE}/Bio/Index/Fastq.pm > ${P5SITE}/Bio/Index/GenBank.pm > -${P5SITE}/Bio/Index/Hmmer.pm > ${P5SITE}/Bio/Index/Qual.pm > -${P5SITE}/Bio/Index/Stockholm.pm > ${P5SITE}/Bio/Index/SwissPfam.pm > ${P5SITE}/Bio/Index/Swissprot.pm > -${P5SITE}/Bio/LiveSeq/ > -${P5SITE}/Bio/LiveSeq/AARange.pm > -${P5SITE}/Bio/LiveSeq/Chain.pm > -${P5SITE}/Bio/LiveSeq/ChainI.pm > -${P5SITE}/Bio/LiveSeq/DNA.pm > -${P5SITE}/Bio/LiveSeq/Exon.pm > -${P5SITE}/Bio/LiveSeq/Gene.pm > -${P5SITE}/Bio/LiveSeq/IO/ > -${P5SITE}/Bio/LiveSeq/IO/BioPerl.pm > -${P5SITE}/Bio/LiveSeq/IO/Loader.pm > -${P5SITE}/Bio/LiveSeq/Intron.pm > -${P5SITE}/Bio/LiveSeq/Mutation.pm > -${P5SITE}/Bio/LiveSeq/Mutator.pm > -${P5SITE}/Bio/LiveSeq/Prim_Transcript.pm > -${P5SITE}/Bio/LiveSeq/Range.pm > -${P5SITE}/Bio/LiveSeq/Repeat_Region.pm > -${P5SITE}/Bio/LiveSeq/Repeat_Unit.pm > -${P5SITE}/Bio/LiveSeq/SeqI.pm > -${P5SITE}/Bio/LiveSeq/Transcript.pm > -${P5SITE}/Bio/LiveSeq/Translation.pm > ${P5SITE}/Bio/LocatableSeq.pm > ${P5SITE}/Bio/Location/ > ${P5SITE}/Bio/Location/Atomic.pm > @@ -384,43 +186,6 @@ ${P5SITE}/Bio/Location/Split.pm > ${P5SITE}/Bio/Location/SplitLocationI.pm > ${P5SITE}/Bio/Location/WidestCoordPolicy.pm > ${P5SITE}/Bio/LocationI.pm > -${P5SITE}/Bio/Map/ > -${P5SITE}/Bio/Map/Clone.pm > -${P5SITE}/Bio/Map/Contig.pm > -${P5SITE}/Bio/Map/CytoMap.pm > -${P5SITE}/Bio/Map/CytoMarker.pm > -${P5SITE}/Bio/Map/CytoPosition.pm > -${P5SITE}/Bio/Map/EntityI.pm > -${P5SITE}/Bio/Map/FPCMarker.pm > -${P5SITE}/Bio/Map/Gene.pm > -${P5SITE}/Bio/Map/GeneMap.pm > -${P5SITE}/Bio/Map/GenePosition.pm > -${P5SITE}/Bio/Map/GeneRelative.pm > -${P5SITE}/Bio/Map/LinkageMap.pm > -${P5SITE}/Bio/Map/LinkagePosition.pm > -${P5SITE}/Bio/Map/MapI.pm > -${P5SITE}/Bio/Map/Mappable.pm > -${P5SITE}/Bio/Map/MappableI.pm > -${P5SITE}/Bio/Map/Marker.pm > -${P5SITE}/Bio/Map/MarkerI.pm > -${P5SITE}/Bio/Map/Microsatellite.pm > -${P5SITE}/Bio/Map/OrderedPosition.pm > -${P5SITE}/Bio/Map/OrderedPositionWithDistance.pm > -${P5SITE}/Bio/Map/Physical.pm > -${P5SITE}/Bio/Map/Position.pm > -${P5SITE}/Bio/Map/PositionHandler.pm > -${P5SITE}/Bio/Map/PositionHandlerI.pm > -${P5SITE}/Bio/Map/PositionI.pm > -${P5SITE}/Bio/Map/PositionWithSequence.pm > -${P5SITE}/Bio/Map/Prediction.pm > -${P5SITE}/Bio/Map/Relative.pm > -${P5SITE}/Bio/Map/RelativeI.pm > -${P5SITE}/Bio/Map/SimpleMap.pm > -${P5SITE}/Bio/Map/TranscriptionFactor.pm > -${P5SITE}/Bio/MapIO/ > -${P5SITE}/Bio/MapIO.pm > -${P5SITE}/Bio/MapIO/fpc.pm > -${P5SITE}/Bio/MapIO/mapmaker.pm > ${P5SITE}/Bio/Matrix/ > ${P5SITE}/Bio/Matrix/Generic.pm > ${P5SITE}/Bio/Matrix/IO/ > @@ -450,11 +215,6 @@ ${P5SITE}/Bio/Matrix/PSM/SiteMatrix.pm > ${P5SITE}/Bio/Matrix/PSM/SiteMatrixI.pm > ${P5SITE}/Bio/Matrix/PhylipDist.pm > ${P5SITE}/Bio/Matrix/Scoring.pm > -${P5SITE}/Bio/MolEvol/ > -${P5SITE}/Bio/MolEvol/CodonModel.pm > -${P5SITE}/Bio/Nexml/ > -${P5SITE}/Bio/Nexml/Factory.pm > -${P5SITE}/Bio/NexmlIO.pm > ${P5SITE}/Bio/Ontology/ > ${P5SITE}/Bio/Ontology/DocumentRegistry.pm > ${P5SITE}/Bio/Ontology/GOterm.pm > @@ -490,75 +250,12 @@ ${P5SITE}/Bio/OntologyIO/obo.pm > ${P5SITE}/Bio/OntologyIO/simplehierarchy.pm > ${P5SITE}/Bio/OntologyIO/soflat.pm > ${P5SITE}/Bio/ParameterBaseI.pm > -${P5SITE}/Bio/Perl.pm > -${P5SITE}/Bio/Phenotype/ > -${P5SITE}/Bio/Phenotype/Correlate.pm > -${P5SITE}/Bio/Phenotype/MeSH/ > -${P5SITE}/Bio/Phenotype/MeSH/Term.pm > -${P5SITE}/Bio/Phenotype/MeSH/Twig.pm > -${P5SITE}/Bio/Phenotype/Measure.pm > -${P5SITE}/Bio/Phenotype/OMIM/ > -${P5SITE}/Bio/Phenotype/OMIM/MiniMIMentry.pm > -${P5SITE}/Bio/Phenotype/OMIM/OMIMentry.pm > -${P5SITE}/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm > -${P5SITE}/Bio/Phenotype/OMIM/OMIMparser.pm > -${P5SITE}/Bio/Phenotype/Phenotype.pm > -${P5SITE}/Bio/Phenotype/PhenotypeI.pm > -${P5SITE}/Bio/PhyloNetwork/ > -${P5SITE}/Bio/PhyloNetwork.pm > -${P5SITE}/Bio/PhyloNetwork/Factory.pm > -${P5SITE}/Bio/PhyloNetwork/FactoryX.pm > -${P5SITE}/Bio/PhyloNetwork/GraphViz.pm > -${P5SITE}/Bio/PhyloNetwork/RandomFactory.pm > -${P5SITE}/Bio/PhyloNetwork/TreeFactory.pm > -${P5SITE}/Bio/PhyloNetwork/TreeFactoryMulti.pm > -${P5SITE}/Bio/PhyloNetwork/TreeFactoryX.pm > -${P5SITE}/Bio/PhyloNetwork/muVector.pm > -${P5SITE}/Bio/PopGen/ > -${P5SITE}/Bio/PopGen/Genotype.pm > -${P5SITE}/Bio/PopGen/GenotypeI.pm > -${P5SITE}/Bio/PopGen/HtSNP.pm > -${P5SITE}/Bio/PopGen/IO/ > -${P5SITE}/Bio/PopGen/IO.pm > -${P5SITE}/Bio/PopGen/IO/csv.pm > -${P5SITE}/Bio/PopGen/IO/hapmap.pm > -${P5SITE}/Bio/PopGen/IO/phase.pm > -${P5SITE}/Bio/PopGen/IO/prettybase.pm > -${P5SITE}/Bio/PopGen/Individual.pm > -${P5SITE}/Bio/PopGen/IndividualI.pm > -${P5SITE}/Bio/PopGen/Marker.pm > -${P5SITE}/Bio/PopGen/MarkerI.pm > -${P5SITE}/Bio/PopGen/PopStats.pm > -${P5SITE}/Bio/PopGen/Population.pm > -${P5SITE}/Bio/PopGen/PopulationI.pm > -${P5SITE}/Bio/PopGen/Simulation/ > -${P5SITE}/Bio/PopGen/Simulation/Coalescent.pm > -${P5SITE}/Bio/PopGen/Simulation/GeneticDrift.pm > -${P5SITE}/Bio/PopGen/Statistics.pm > -${P5SITE}/Bio/PopGen/TagHaplotype.pm > -${P5SITE}/Bio/PopGen/Utilities.pm > ${P5SITE}/Bio/PrimarySeq.pm > ${P5SITE}/Bio/PrimarySeqI.pm > ${P5SITE}/Bio/PullParserI.pm > ${P5SITE}/Bio/Range.pm > ${P5SITE}/Bio/RangeI.pm > -${P5SITE}/Bio/Restriction/ > -${P5SITE}/Bio/Restriction/Analysis.pm > -${P5SITE}/Bio/Restriction/Enzyme/ > -${P5SITE}/Bio/Restriction/Enzyme.pm > -${P5SITE}/Bio/Restriction/Enzyme/MultiCut.pm > -${P5SITE}/Bio/Restriction/Enzyme/MultiSite.pm > -${P5SITE}/Bio/Restriction/EnzymeCollection.pm > -${P5SITE}/Bio/Restriction/EnzymeI.pm > -${P5SITE}/Bio/Restriction/IO/ > -${P5SITE}/Bio/Restriction/IO.pm > -${P5SITE}/Bio/Restriction/IO/bairoch.pm > -${P5SITE}/Bio/Restriction/IO/base.pm > -${P5SITE}/Bio/Restriction/IO/itype2.pm > -${P5SITE}/Bio/Restriction/IO/prototype.pm > -${P5SITE}/Bio/Restriction/IO/withrefm.pm > ${P5SITE}/Bio/Root/ > -${P5SITE}/Bio/Root/Build.pm > ${P5SITE}/Bio/Root/Exception.pm > ${P5SITE}/Bio/Root/HTTPget.pm > ${P5SITE}/Bio/Root/IO.pm > @@ -566,6 +263,7 @@ ${P5SITE}/Bio/Root/Root.pm > ${P5SITE}/Bio/Root/RootI.pm > ${P5SITE}/Bio/Root/Storable.pm > ${P5SITE}/Bio/Root/Test.pm > +${P5SITE}/Bio/Root/TestObject.pm > ${P5SITE}/Bio/Root/Utilities.pm > ${P5SITE}/Bio/Root/Version.pm > ${P5SITE}/Bio/Search/ > @@ -579,10 +277,8 @@ ${P5SITE}/Bio/Search/HSP/BlastHSP.pm > ${P5SITE}/Bio/Search/HSP/BlastPullHSP.pm > ${P5SITE}/Bio/Search/HSP/FastaHSP.pm > ${P5SITE}/Bio/Search/HSP/GenericHSP.pm > -${P5SITE}/Bio/Search/HSP/HMMERHSP.pm > ${P5SITE}/Bio/Search/HSP/HSPFactory.pm > ${P5SITE}/Bio/Search/HSP/HSPI.pm > -${P5SITE}/Bio/Search/HSP/HmmpfamHSP.pm > ${P5SITE}/Bio/Search/HSP/ModelHSP.pm > ${P5SITE}/Bio/Search/HSP/PSLHSP.pm > ${P5SITE}/Bio/Search/HSP/PsiBlastHSP.pm > @@ -593,14 +289,11 @@ ${P5SITE}/Bio/Search/Hit/BlastHit.pm > ${P5SITE}/Bio/Search/Hit/BlastPullHit.pm > ${P5SITE}/Bio/Search/Hit/Fasta.pm > ${P5SITE}/Bio/Search/Hit/GenericHit.pm > -${P5SITE}/Bio/Search/Hit/HMMERHit.pm > ${P5SITE}/Bio/Search/Hit/HitFactory.pm > ${P5SITE}/Bio/Search/Hit/HitI.pm > -${P5SITE}/Bio/Search/Hit/HmmpfamHit.pm > ${P5SITE}/Bio/Search/Hit/ModelHit.pm > ${P5SITE}/Bio/Search/Hit/PsiBlastHit.pm > ${P5SITE}/Bio/Search/Hit/PullHitI.pm > -${P5SITE}/Bio/Search/Hit/hmmer3Hit.pm > ${P5SITE}/Bio/Search/Iteration/ > ${P5SITE}/Bio/Search/Iteration/GenericIteration.pm > ${P5SITE}/Bio/Search/Iteration/IterationI.pm > @@ -610,20 +303,17 @@ ${P5SITE}/Bio/Search/Result/BlastPullRes > ${P5SITE}/Bio/Search/Result/BlastResult.pm > ${P5SITE}/Bio/Search/Result/CrossMatchResult.pm > ${P5SITE}/Bio/Search/Result/GenericResult.pm > -${P5SITE}/Bio/Search/Result/HMMERResult.pm > -${P5SITE}/Bio/Search/Result/HmmpfamResult.pm > +${P5SITE}/Bio/Search/Result/INFERNALResult.pm > ${P5SITE}/Bio/Search/Result/PullResultI.pm > ${P5SITE}/Bio/Search/Result/ResultFactory.pm > ${P5SITE}/Bio/Search/Result/ResultI.pm > ${P5SITE}/Bio/Search/Result/WABAResult.pm > -${P5SITE}/Bio/Search/Result/hmmer3Result.pm > ${P5SITE}/Bio/Search/SearchUtils.pm > ${P5SITE}/Bio/Search/StatisticsI.pm > ${P5SITE}/Bio/Search/Tiling/ > ${P5SITE}/Bio/Search/Tiling/MapTileUtils.pm > ${P5SITE}/Bio/Search/Tiling/MapTiling.pm > ${P5SITE}/Bio/Search/Tiling/TilingI.pm > -${P5SITE}/Bio/SearchDist.pm > ${P5SITE}/Bio/SearchIO/ > ${P5SITE}/Bio/SearchIO.pm > ${P5SITE}/Bio/SearchIO/EventHandlerI.pm > @@ -632,30 +322,21 @@ ${P5SITE}/Bio/SearchIO/IteratedSearchRes > ${P5SITE}/Bio/SearchIO/SearchResultEventBuilder.pm > ${P5SITE}/Bio/SearchIO/SearchWriterI.pm > ${P5SITE}/Bio/SearchIO/Writer/ > -${P5SITE}/Bio/SearchIO/Writer/BSMLResultWriter.pm > ${P5SITE}/Bio/SearchIO/Writer/GbrowseGFF.pm > ${P5SITE}/Bio/SearchIO/Writer/HSPTableWriter.pm > ${P5SITE}/Bio/SearchIO/Writer/HTMLResultWriter.pm > ${P5SITE}/Bio/SearchIO/Writer/HitTableWriter.pm > ${P5SITE}/Bio/SearchIO/Writer/ResultTableWriter.pm > ${P5SITE}/Bio/SearchIO/Writer/TextResultWriter.pm > -${P5SITE}/Bio/SearchIO/XML/ > -${P5SITE}/Bio/SearchIO/XML/BlastHandler.pm > -${P5SITE}/Bio/SearchIO/XML/PsiBlastHandler.pm > ${P5SITE}/Bio/SearchIO/axt.pm > ${P5SITE}/Bio/SearchIO/blast.pm > ${P5SITE}/Bio/SearchIO/blast_pull.pm > ${P5SITE}/Bio/SearchIO/blasttable.pm > -${P5SITE}/Bio/SearchIO/blastxml.pm > ${P5SITE}/Bio/SearchIO/cross_match.pm > ${P5SITE}/Bio/SearchIO/erpin.pm > ${P5SITE}/Bio/SearchIO/exonerate.pm > ${P5SITE}/Bio/SearchIO/fasta.pm > ${P5SITE}/Bio/SearchIO/gmap_f9.pm > -${P5SITE}/Bio/SearchIO/hmmer.pm > -${P5SITE}/Bio/SearchIO/hmmer2.pm > -${P5SITE}/Bio/SearchIO/hmmer3.pm > -${P5SITE}/Bio/SearchIO/hmmer_pull.pm > ${P5SITE}/Bio/SearchIO/infernal.pm > ${P5SITE}/Bio/SearchIO/megablast.pm > ${P5SITE}/Bio/SearchIO/psl.pm > @@ -684,15 +365,10 @@ ${P5SITE}/Bio/Seq/RichSeqI.pm > ${P5SITE}/Bio/Seq/SeqBuilder.pm > ${P5SITE}/Bio/Seq/SeqFactory.pm > ${P5SITE}/Bio/Seq/SeqFastaSpeedFactory.pm > -${P5SITE}/Bio/Seq/SeqWithQuality.pm > ${P5SITE}/Bio/Seq/SequenceTrace.pm > ${P5SITE}/Bio/Seq/SimulatedRead.pm > ${P5SITE}/Bio/Seq/TraceI.pm > ${P5SITE}/Bio/SeqAnalysisParserI.pm > -${P5SITE}/Bio/SeqEvolution/ > -${P5SITE}/Bio/SeqEvolution/DNAPoint.pm > -${P5SITE}/Bio/SeqEvolution/EvolutionI.pm > -${P5SITE}/Bio/SeqEvolution/Factory.pm > ${P5SITE}/Bio/SeqFeature/ > ${P5SITE}/Bio/SeqFeature/Amplicon.pm > ${P5SITE}/Bio/SeqFeature/AnnotationAdaptor.pm > @@ -716,9 +392,6 @@ ${P5SITE}/Bio/SeqFeature/Generic.pm > ${P5SITE}/Bio/SeqFeature/Lite.pm > ${P5SITE}/Bio/SeqFeature/PositionProxy.pm > ${P5SITE}/Bio/SeqFeature/Primer.pm > -${P5SITE}/Bio/SeqFeature/SiRNA/ > -${P5SITE}/Bio/SeqFeature/SiRNA/Oligo.pm > -${P5SITE}/Bio/SeqFeature/SiRNA/Pair.pm > ${P5SITE}/Bio/SeqFeature/Similarity.pm > ${P5SITE}/Bio/SeqFeature/SimilarityPair.pm > ${P5SITE}/Bio/SeqFeature/SubSeq.pm > @@ -736,25 +409,14 @@ ${P5SITE}/Bio/SeqIO/FTHelper.pm > ${P5SITE}/Bio/SeqIO/Handler/ > ${P5SITE}/Bio/SeqIO/Handler/GenericRichSeqHandler.pm > ${P5SITE}/Bio/SeqIO/MultiFile.pm > -${P5SITE}/Bio/SeqIO/abi.pm > ${P5SITE}/Bio/SeqIO/ace.pm > -${P5SITE}/Bio/SeqIO/agave.pm > -${P5SITE}/Bio/SeqIO/alf.pm > ${P5SITE}/Bio/SeqIO/asciitree.pm > ${P5SITE}/Bio/SeqIO/bsml.pm > ${P5SITE}/Bio/SeqIO/bsml_sax.pm > -${P5SITE}/Bio/SeqIO/chadoxml.pm > -${P5SITE}/Bio/SeqIO/chaos.pm > -${P5SITE}/Bio/SeqIO/chaosxml.pm > -${P5SITE}/Bio/SeqIO/ctf.pm > ${P5SITE}/Bio/SeqIO/embl.pm > ${P5SITE}/Bio/SeqIO/embldriver.pm > -${P5SITE}/Bio/SeqIO/entrezgene.pm > -${P5SITE}/Bio/SeqIO/excel.pm > -${P5SITE}/Bio/SeqIO/exp.pm > ${P5SITE}/Bio/SeqIO/fasta.pm > ${P5SITE}/Bio/SeqIO/fastq.pm > -${P5SITE}/Bio/SeqIO/flybase_chadoxml.pm > ${P5SITE}/Bio/SeqIO/game/ > ${P5SITE}/Bio/SeqIO/game.pm > ${P5SITE}/Bio/SeqIO/game/featHandler.pm > @@ -769,20 +431,16 @@ ${P5SITE}/Bio/SeqIO/genbank.pm > ${P5SITE}/Bio/SeqIO/interpro.pm > ${P5SITE}/Bio/SeqIO/kegg.pm > ${P5SITE}/Bio/SeqIO/largefasta.pm > -${P5SITE}/Bio/SeqIO/lasergene.pm > ${P5SITE}/Bio/SeqIO/locuslink.pm > ${P5SITE}/Bio/SeqIO/mbsout.pm > ${P5SITE}/Bio/SeqIO/metafasta.pm > ${P5SITE}/Bio/SeqIO/msout.pm > -${P5SITE}/Bio/SeqIO/nexml.pm > ${P5SITE}/Bio/SeqIO/phd.pm > ${P5SITE}/Bio/SeqIO/pir.pm > -${P5SITE}/Bio/SeqIO/pln.pm > ${P5SITE}/Bio/SeqIO/qual.pm > ${P5SITE}/Bio/SeqIO/raw.pm > ${P5SITE}/Bio/SeqIO/scf.pm > ${P5SITE}/Bio/SeqIO/seqxml.pm > -${P5SITE}/Bio/SeqIO/strider.pm > ${P5SITE}/Bio/SeqIO/swiss.pm > ${P5SITE}/Bio/SeqIO/swissdriver.pm > ${P5SITE}/Bio/SeqIO/tab.pm > @@ -792,58 +450,17 @@ ${P5SITE}/Bio/SeqIO/tigrxml.pm > ${P5SITE}/Bio/SeqIO/tinyseq/ > ${P5SITE}/Bio/SeqIO/tinyseq.pm > ${P5SITE}/Bio/SeqIO/tinyseq/tinyseqHandler.pm > -${P5SITE}/Bio/SeqIO/ztr.pm > ${P5SITE}/Bio/SeqUtils.pm > ${P5SITE}/Bio/SimpleAlign.pm > ${P5SITE}/Bio/SimpleAnalysisI.pm > ${P5SITE}/Bio/Species.pm > -${P5SITE}/Bio/Structure/ > -${P5SITE}/Bio/Structure/Atom.pm > -${P5SITE}/Bio/Structure/Chain.pm > -${P5SITE}/Bio/Structure/Entry.pm > -${P5SITE}/Bio/Structure/IO/ > -${P5SITE}/Bio/Structure/IO.pm > -${P5SITE}/Bio/Structure/IO/pdb.pm > -${P5SITE}/Bio/Structure/Model.pm > -${P5SITE}/Bio/Structure/Residue.pm > -${P5SITE}/Bio/Structure/SecStr/ > -${P5SITE}/Bio/Structure/SecStr/DSSP/ > -${P5SITE}/Bio/Structure/SecStr/DSSP/Res.pm > -${P5SITE}/Bio/Structure/SecStr/STRIDE/ > -${P5SITE}/Bio/Structure/SecStr/STRIDE/Res.pm > -${P5SITE}/Bio/Structure/StructureI.pm > -${P5SITE}/Bio/Symbol/ > -${P5SITE}/Bio/Symbol/Alphabet.pm > -${P5SITE}/Bio/Symbol/AlphabetI.pm > -${P5SITE}/Bio/Symbol/DNAAlphabet.pm > -${P5SITE}/Bio/Symbol/ProteinAlphabet.pm > -${P5SITE}/Bio/Symbol/Symbol.pm > -${P5SITE}/Bio/Symbol/SymbolI.pm > ${P5SITE}/Bio/Taxon.pm > -${P5SITE}/Bio/Taxonomy/ > -${P5SITE}/Bio/Taxonomy.pm > -${P5SITE}/Bio/Taxonomy/FactoryI.pm > -${P5SITE}/Bio/Taxonomy/Node.pm > -${P5SITE}/Bio/Taxonomy/Taxon.pm > -${P5SITE}/Bio/Taxonomy/Tree.pm > ${P5SITE}/Bio/Tools/ > -${P5SITE}/Bio/Tools/AlignFactory.pm > ${P5SITE}/Bio/Tools/Alignment/ > ${P5SITE}/Bio/Tools/Alignment/Consed.pm > ${P5SITE}/Bio/Tools/Alignment/Trim.pm > ${P5SITE}/Bio/Tools/AmpliconSearch.pm > ${P5SITE}/Bio/Tools/Analysis/ > -${P5SITE}/Bio/Tools/Analysis/DNA/ > -${P5SITE}/Bio/Tools/Analysis/DNA/ESEfinder.pm > -${P5SITE}/Bio/Tools/Analysis/Protein/ > -${P5SITE}/Bio/Tools/Analysis/Protein/Domcut.pm > -${P5SITE}/Bio/Tools/Analysis/Protein/ELM.pm > -${P5SITE}/Bio/Tools/Analysis/Protein/GOR4.pm > -${P5SITE}/Bio/Tools/Analysis/Protein/HNN.pm > -${P5SITE}/Bio/Tools/Analysis/Protein/Mitoprot.pm > -${P5SITE}/Bio/Tools/Analysis/Protein/NetPhos.pm > -${P5SITE}/Bio/Tools/Analysis/Protein/Scansite.pm > -${P5SITE}/Bio/Tools/Analysis/Protein/Sopma.pm > ${P5SITE}/Bio/Tools/Analysis/SimpleAnalysisBase.pm > ${P5SITE}/Bio/Tools/AnalysisResult.pm > ${P5SITE}/Bio/Tools/Blat.pm > @@ -853,14 +470,12 @@ ${P5SITE}/Bio/Tools/ECnumber.pm > ${P5SITE}/Bio/Tools/EMBOSS/ > ${P5SITE}/Bio/Tools/EMBOSS/Palindrome.pm > ${P5SITE}/Bio/Tools/EPCR.pm > -${P5SITE}/Bio/Tools/ERPIN.pm > ${P5SITE}/Bio/Tools/ESTScan.pm > ${P5SITE}/Bio/Tools/Eponine.pm > ${P5SITE}/Bio/Tools/Est2Genome.pm > ${P5SITE}/Bio/Tools/Fgenesh.pm > ${P5SITE}/Bio/Tools/FootPrinter.pm > ${P5SITE}/Bio/Tools/GFF.pm > -${P5SITE}/Bio/Tools/Gel.pm > ${P5SITE}/Bio/Tools/Geneid.pm > ${P5SITE}/Bio/Tools/Genemark.pm > ${P5SITE}/Bio/Tools/Genewise.pm > @@ -869,28 +484,16 @@ ${P5SITE}/Bio/Tools/Genscan.pm > ${P5SITE}/Bio/Tools/Glimmer.pm > ${P5SITE}/Bio/Tools/Grail.pm > ${P5SITE}/Bio/Tools/GuessSeqFormat.pm > -${P5SITE}/Bio/Tools/HMMER/ > -${P5SITE}/Bio/Tools/HMMER/Domain.pm > -${P5SITE}/Bio/Tools/HMMER/Results.pm > -${P5SITE}/Bio/Tools/HMMER/Set.pm > -${P5SITE}/Bio/Tools/Hmmpfam.pm > ${P5SITE}/Bio/Tools/IUPAC.pm > -${P5SITE}/Bio/Tools/Infernal.pm > ${P5SITE}/Bio/Tools/Lucy.pm > ${P5SITE}/Bio/Tools/MZEF.pm > ${P5SITE}/Bio/Tools/Match.pm > ${P5SITE}/Bio/Tools/OddCodes.pm > ${P5SITE}/Bio/Tools/Phylo/ > ${P5SITE}/Bio/Tools/Phylo/Gerp.pm > -${P5SITE}/Bio/Tools/Phylo/Gumby.pm > ${P5SITE}/Bio/Tools/Phylo/Molphy/ > ${P5SITE}/Bio/Tools/Phylo/Molphy.pm > ${P5SITE}/Bio/Tools/Phylo/Molphy/Result.pm > -${P5SITE}/Bio/Tools/Phylo/PAML/ > -${P5SITE}/Bio/Tools/Phylo/PAML.pm > -${P5SITE}/Bio/Tools/Phylo/PAML/Codeml.pm > -${P5SITE}/Bio/Tools/Phylo/PAML/ModelResult.pm > -${P5SITE}/Bio/Tools/Phylo/PAML/Result.pm > ${P5SITE}/Bio/Tools/Phylo/Phylip/ > ${P5SITE}/Bio/Tools/Phylo/Phylip/ProtDist.pm > ${P5SITE}/Bio/Tools/Prediction/ > @@ -907,34 +510,26 @@ ${P5SITE}/Bio/Tools/Prints.pm > ${P5SITE}/Bio/Tools/Profile.pm > ${P5SITE}/Bio/Tools/Promoterwise.pm > ${P5SITE}/Bio/Tools/PrositeScan.pm > -${P5SITE}/Bio/Tools/Protparam.pm > ${P5SITE}/Bio/Tools/Pseudowise.pm > ${P5SITE}/Bio/Tools/QRNA.pm > -${P5SITE}/Bio/Tools/RNAMotif.pm > ${P5SITE}/Bio/Tools/RandomDistFunctions.pm > ${P5SITE}/Bio/Tools/RepeatMasker.pm > ${P5SITE}/Bio/Tools/Run/ > +${P5SITE}/Bio/Tools/Run/Analysis.pm > +${P5SITE}/Bio/Tools/Run/AnalysisFactory.pm > ${P5SITE}/Bio/Tools/Run/GenericParameters.pm > ${P5SITE}/Bio/Tools/Run/ParametersI.pm > -${P5SITE}/Bio/Tools/Run/RemoteBlast.pm > -${P5SITE}/Bio/Tools/Run/StandAloneBlast.pm > -${P5SITE}/Bio/Tools/Run/StandAloneNCBIBlast.pm > -${P5SITE}/Bio/Tools/Run/StandAloneWUBlast.pm > +${P5SITE}/Bio/Tools/Run/Phylo/ > +${P5SITE}/Bio/Tools/Run/Phylo/PhyloBase.pm > ${P5SITE}/Bio/Tools/Run/WrapperBase/ > ${P5SITE}/Bio/Tools/Run/WrapperBase.pm > ${P5SITE}/Bio/Tools/Run/WrapperBase/CommandExts.pm > -${P5SITE}/Bio/Tools/Run/hmmer3.pm > ${P5SITE}/Bio/Tools/Seg.pm > ${P5SITE}/Bio/Tools/SeqPattern/ > ${P5SITE}/Bio/Tools/SeqPattern.pm > ${P5SITE}/Bio/Tools/SeqPattern/Backtranslate.pm > ${P5SITE}/Bio/Tools/SeqStats.pm > ${P5SITE}/Bio/Tools/SeqWords.pm > -${P5SITE}/Bio/Tools/SiRNA/ > -${P5SITE}/Bio/Tools/SiRNA.pm > -${P5SITE}/Bio/Tools/SiRNA/Ruleset/ > -${P5SITE}/Bio/Tools/SiRNA/Ruleset/saigo.pm > -${P5SITE}/Bio/Tools/SiRNA/Ruleset/tuschl.pm > ${P5SITE}/Bio/Tools/Sigcleave.pm > ${P5SITE}/Bio/Tools/Signalp/ > ${P5SITE}/Bio/Tools/Signalp.pm > @@ -948,19 +543,14 @@ ${P5SITE}/Bio/Tools/Spidey/Results.pm > ${P5SITE}/Bio/Tools/TandemRepeatsFinder.pm > ${P5SITE}/Bio/Tools/TargetP.pm > ${P5SITE}/Bio/Tools/Tmhmm.pm > -${P5SITE}/Bio/Tools/dpAlign.pm > ${P5SITE}/Bio/Tools/ipcress.pm > ${P5SITE}/Bio/Tools/isPcr.pm > ${P5SITE}/Bio/Tools/pICalculator.pm > -${P5SITE}/Bio/Tools/pSW.pm > ${P5SITE}/Bio/Tools/tRNAscanSE.pm > ${P5SITE}/Bio/Tree/ > -${P5SITE}/Bio/Tree/AlleleNode.pm > ${P5SITE}/Bio/Tree/AnnotatableNode.pm > ${P5SITE}/Bio/Tree/Compatible.pm > ${P5SITE}/Bio/Tree/DistanceFactory.pm > -${P5SITE}/Bio/Tree/Draw/ > -${P5SITE}/Bio/Tree/Draw/Cladogram.pm > ${P5SITE}/Bio/Tree/Node.pm > ${P5SITE}/Bio/Tree/NodeI.pm > ${P5SITE}/Bio/Tree/NodeNHX.pm > @@ -976,94 +566,56 @@ ${P5SITE}/Bio/TreeIO/TreeEventBuilder.pm > ${P5SITE}/Bio/TreeIO/cluster.pm > ${P5SITE}/Bio/TreeIO/lintree.pm > ${P5SITE}/Bio/TreeIO/newick.pm > -${P5SITE}/Bio/TreeIO/nexml.pm > ${P5SITE}/Bio/TreeIO/nexus.pm > ${P5SITE}/Bio/TreeIO/nhx.pm > ${P5SITE}/Bio/TreeIO/pag.pm > ${P5SITE}/Bio/TreeIO/phyloxml.pm > -${P5SITE}/Bio/TreeIO/svggraph.pm > ${P5SITE}/Bio/TreeIO/tabtree.pm > ${P5SITE}/Bio/UpdateableSeqI.pm > -${P5SITE}/Bio/Variation/ > -${P5SITE}/Bio/Variation/AAChange.pm > -${P5SITE}/Bio/Variation/AAReverseMutate.pm > -${P5SITE}/Bio/Variation/Allele.pm > -${P5SITE}/Bio/Variation/DNAMutation.pm > -${P5SITE}/Bio/Variation/IO/ > -${P5SITE}/Bio/Variation/IO.pm > -${P5SITE}/Bio/Variation/IO/flat.pm > -${P5SITE}/Bio/Variation/IO/xml.pm > -${P5SITE}/Bio/Variation/RNAChange.pm > -${P5SITE}/Bio/Variation/SNP.pm > -${P5SITE}/Bio/Variation/SeqDiff.pm > -${P5SITE}/Bio/Variation/VariantI.pm > ${P5SITE}/Bio/WebAgent.pm > -@man man/man1/bp_aacomp.pl.1 > -@man man/man1/bp_biofetch_genbank_proxy.pl.1 > -@man man/man1/bp_bioflat_index.pl.1 > -@man man/man1/bp_biogetseq.pl.1 > -@man man/man1/bp_blast2tree.pl.1 > -@man man/man1/bp_bulk_load_gff.pl.1 > -@man man/man1/bp_chaos_plot.pl.1 > -@man man/man1/bp_classify_hits_kingdom.pl.1 > -@man man/man1/bp_composite_LD.pl.1 > -@man man/man1/bp_dbsplit.pl.1 > -@man man/man1/bp_download_query_genbank.pl.1 > -@man man/man1/bp_extract_feature_seq.pl.1 > -@man man/man1/bp_fast_load_gff.pl.1 > -@man man/man1/bp_fastam9_to_table.pl.1 > -@man man/man1/bp_fetch.pl.1 > -@man man/man1/bp_filter_search.pl.1 > -@man man/man1/bp_flanks.pl.1 > -@man man/man1/bp_gccalc.pl.1 > -@man man/man1/bp_genbank2gff.pl.1 > -@man man/man1/bp_genbank2gff3.pl.1 > -@man man/man1/bp_generate_histogram.pl.1 > -@man man/man1/bp_heterogeneity_test.pl.1 > -@man man/man1/bp_hivq.pl.1 > -@man man/man1/bp_hmmer_to_table.pl.1 > -@man man/man1/bp_index.pl.1 > -@man man/man1/bp_load_gff.pl.1 > -@man man/man1/bp_local_taxonomydb_query.pl.1 > -@man man/man1/bp_make_mrna_protein.pl.1 > -@man man/man1/bp_mask_by_search.pl.1 > -@man man/man1/bp_meta_gff.pl.1 > -@man man/man1/bp_mrtrans.pl.1 > -@man man/man1/bp_mutate.pl.1 > -@man man/man1/bp_netinstall.pl.1 > -@man man/man1/bp_nexus2nh.pl.1 > -@man man/man1/bp_nrdb.pl.1 > -@man man/man1/bp_oligo_count.pl.1 > -@man man/man1/bp_pairwise_kaks.pl.1 > -@man man/man1/bp_parse_hmmsearch.pl.1 > -@man man/man1/bp_process_gadfly.pl.1 > -@man man/man1/bp_process_sgd.pl.1 > -@man man/man1/bp_process_wormbase.pl.1 > -@man man/man1/bp_query_entrez_taxa.pl.1 > -@man man/man1/bp_remote_blast.pl.1 > -@man man/man1/bp_revtrans-motif.pl.1 > -@man man/man1/bp_search2BSML.pl.1 > -@man man/man1/bp_search2alnblocks.pl.1 > -@man man/man1/bp_search2gff.pl.1 > -@man man/man1/bp_search2table.pl.1 > -@man man/man1/bp_search2tribe.pl.1 > -@man man/man1/bp_seq_length.pl.1 > -@man man/man1/bp_seqconvert.pl.1 > -@man man/man1/bp_seqcut.pl.1 > -@man man/man1/bp_seqfeature_load.pl.1 > -@man man/man1/bp_seqpart.pl.1 > -@man man/man1/bp_seqret.pl.1 > -@man man/man1/bp_seqretsplit.pl.1 > -@man man/man1/bp_split_seq.pl.1 > -@man man/man1/bp_sreformat.pl.1 > -@man man/man1/bp_taxid4species.pl.1 > -@man man/man1/bp_taxonomy2tree.pl.1 > -@man man/man1/bp_translate_seq.pl.1 > -@man man/man1/bp_tree2pag.pl.1 > -@man man/man1/bp_unflatten_seq.pl.1 > +${P5SITE}/BioPerl.pm > +@man man/man1/bp_aacomp.1 > +@man man/man1/bp_bioflat_index.1 > +@man man/man1/bp_biogetseq.1 > +@man man/man1/bp_dbsplit.1 > +@man man/man1/bp_extract_feature_seq.1 > +@man man/man1/bp_fastam9_to_table.1 > +@man man/man1/bp_fetch.1 > +@man man/man1/bp_filter_search.1 > +@man man/man1/bp_find-blast-matches.1 > +@man man/man1/bp_gccalc.1 > +@man man/man1/bp_genbank2gff3.1 > +@man man/man1/bp_index.1 > +@man man/man1/bp_local_taxonomydb_query.1 > +@man man/man1/bp_make_mrna_protein.1 > +@man man/man1/bp_mask_by_search.1 > +@man man/man1/bp_mrtrans.1 > +@man man/man1/bp_mutate.1 > +@man man/man1/bp_nexus2nh.1 > +@man man/man1/bp_nrdb.1 > +@man man/man1/bp_oligo_count.1 > +@man man/man1/bp_process_gadfly.1 > +@man man/man1/bp_process_sgd.1 > +@man man/man1/bp_revtrans-motif.1 > +@man man/man1/bp_search2alnblocks.1 > +@man man/man1/bp_search2gff.1 > +@man man/man1/bp_search2table.1 > +@man man/man1/bp_search2tribe.1 > +@man man/man1/bp_seq_length.1 > +@man man/man1/bp_seqconvert.1 > +@man man/man1/bp_seqcut.1 > +@man man/man1/bp_seqpart.1 > +@man man/man1/bp_seqret.1 > +@man man/man1/bp_seqretsplit.1 > +@man man/man1/bp_split_seq.1 > +@man man/man1/bp_sreformat.1 > +@man man/man1/bp_taxid4species.1 > +@man man/man1/bp_taxonomy2tree.1 > +@man man/man1/bp_translate_seq.1 > +@man man/man1/bp_tree2pag.1 > +@man man/man1/bp_unflatten_seq.1 > @man man/man3p/Bio::Align::AlignI.3p > @man man/man3p/Bio::Align::DNAStatistics.3p > -@man man/man3p/Bio::Align::Graphics.3p > @man man/man3p/Bio::Align::PairwiseStatistics.3p > @man man/man3p/Bio::Align::ProteinStatistics.3p > @man man/man3p/Bio::Align::StatisticsI.3p > @@ -1082,7 +634,6 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::AlignIO::meme.3p > @man man/man3p/Bio::AlignIO::metafasta.3p > @man man/man3p/Bio::AlignIO::msf.3p > -@man man/man3p/Bio::AlignIO::nexml.3p > @man man/man3p/Bio::AlignIO::nexus.3p > @man man/man3p/Bio::AlignIO::pfam.3p > @man man/man3p/Bio::AlignIO::phylip.3p > @@ -1091,7 +642,6 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::AlignIO::prodom.3p > @man man/man3p/Bio::AlignIO::psi.3p > @man man/man3p/Bio::AlignIO::selex.3p > -@man man/man3p/Bio::AlignIO::stockholm.3p > @man man/man3p/Bio::AlignIO::xmfa.3p > @man man/man3p/Bio::AnalysisI.3p > @man man/man3p/Bio::AnalysisParserI.3p > @@ -1112,50 +662,9 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Annotation::TypeManager.3p > @man man/man3p/Bio::AnnotationCollectionI.3p > @man man/man3p/Bio::AnnotationI.3p > -@man man/man3p/Bio::Assembly::Contig.3p > -@man man/man3p/Bio::Assembly::ContigAnalysis.3p > -@man man/man3p/Bio::Assembly::IO.3p > -@man man/man3p/Bio::Assembly::IO::ace.3p > -@man man/man3p/Bio::Assembly::IO::bowtie.3p > -@man man/man3p/Bio::Assembly::IO::maq.3p > -@man man/man3p/Bio::Assembly::IO::phrap.3p > -@man man/man3p/Bio::Assembly::IO::sam.3p > -@man man/man3p/Bio::Assembly::IO::tigr.3p > -@man man/man3p/Bio::Assembly::Scaffold.3p > -@man man/man3p/Bio::Assembly::ScaffoldI.3p > -@man man/man3p/Bio::Assembly::Singlet.3p > -@man man/man3p/Bio::Assembly::Tools::ContigSpectrum.3p > -@man man/man3p/Bio::Cluster::ClusterFactory.3p > -@man man/man3p/Bio::Cluster::FamilyI.3p > -@man man/man3p/Bio::Cluster::SequenceFamily.3p > -@man man/man3p/Bio::Cluster::UniGene.3p > -@man man/man3p/Bio::Cluster::UniGeneI.3p > -@man man/man3p/Bio::ClusterI.3p > -@man man/man3p/Bio::ClusterIO.3p > -@man man/man3p/Bio::ClusterIO::dbsnp.3p > -@man man/man3p/Bio::ClusterIO::unigene.3p > @man man/man3p/Bio::CodonUsage::IO.3p > @man man/man3p/Bio::CodonUsage::Table.3p > -@man man/man3p/Bio::Coordinate::Chain.3p > -@man man/man3p/Bio::Coordinate::Collection.3p > -@man man/man3p/Bio::Coordinate::ExtrapolatingPair.3p > -@man man/man3p/Bio::Coordinate::GeneMapper.3p > -@man man/man3p/Bio::Coordinate::Graph.3p > -@man man/man3p/Bio::Coordinate::MapperI.3p > -@man man/man3p/Bio::Coordinate::Pair.3p > -@man man/man3p/Bio::Coordinate::Result.3p > -@man man/man3p/Bio::Coordinate::Result::Gap.3p > -@man man/man3p/Bio::Coordinate::Result::Match.3p > -@man man/man3p/Bio::Coordinate::ResultI.3p > -@man man/man3p/Bio::Coordinate::Utils.3p > -@man man/man3p/Bio::DB::Ace.3p > -@man man/man3p/Bio::DB::BioFetch.3p > -@man man/man3p/Bio::DB::CUTG.3p > @man man/man3p/Bio::DB::DBFetch.3p > -@man man/man3p/Bio::DB::EMBL.3p > -@man man/man3p/Bio::DB::EntrezGene.3p > -@man man/man3p/Bio::DB::Expression.3p > -@man man/man3p/Bio::DB::Expression::geo.3p > @man man/man3p/Bio::DB::Failover.3p > @man man/man3p/Bio::DB::Fasta.3p > @man man/man3p/Bio::DB::FileCache.3p > @@ -1166,107 +675,24 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::DB::Flat::BDB::genbank.3p > @man man/man3p/Bio::DB::Flat::BDB::swiss.3p > @man man/man3p/Bio::DB::Flat::BinarySearch.3p > -@man man/man3p/Bio::DB::GFF.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::ace.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::berkeleydb.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::berkeleydb::iterator.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::biofetch.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::biofetch_oracle.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::dbi.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::dbi::caching_handle.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::dbi::iterator.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::dbi::mysql.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::dbi::mysqlace.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::dbi::mysqlcmap.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::dbi::mysqlopt.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::dbi::oracle.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::dbi::oracleace.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::dbi::pg.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::dbi::pg_fts.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::memory.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::memory::feature_serializer.3p > -@man man/man3p/Bio::DB::GFF::Adaptor::memory::iterator.3p > -@man man/man3p/Bio::DB::GFF::Aggregator.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::alignment.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::clone.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::coding.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::gene.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::match.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::none.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::orf.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::processed_transcript.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::so_transcript.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::transcript.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::ucsc_acembly.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::ucsc_ensgene.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::ucsc_genscan.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::ucsc_refgene.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::ucsc_sanger22.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::ucsc_softberry.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::ucsc_twinscan.3p > -@man man/man3p/Bio::DB::GFF::Aggregator::ucsc_unigene.3p > -@man man/man3p/Bio::DB::GFF::Featname.3p > -@man man/man3p/Bio::DB::GFF::Feature.3p > -@man man/man3p/Bio::DB::GFF::Homol.3p > -@man man/man3p/Bio::DB::GFF::RelSegment.3p > -@man man/man3p/Bio::DB::GFF::Segment.3p > -@man man/man3p/Bio::DB::GFF::Typename.3p > @man man/man3p/Bio::DB::GFF::Util::Binning.3p > @man man/man3p/Bio::DB::GFF::Util::Rearrange.3p > -@man man/man3p/Bio::DB::GenBank.3p > -@man man/man3p/Bio::DB::GenPept.3p > @man man/man3p/Bio::DB::GenericWebAgent.3p > -@man man/man3p/Bio::DB::HIV.3p > -@man man/man3p/Bio::DB::HIV::HIVAnnotProcessor.3p > -@man man/man3p/Bio::DB::HIV::HIVQueryHelper.3p > @man man/man3p/Bio::DB::InMemoryCache.3p > @man man/man3p/Bio::DB::IndexedBase.3p > @man man/man3p/Bio::DB::LocationI.3p > -@man man/man3p/Bio::DB::MeSH.3p > -@man man/man3p/Bio::DB::NCBIHelper.3p > @man man/man3p/Bio::DB::Qual.3p > -@man man/man3p/Bio::DB::Query::GenBank.3p > -@man man/man3p/Bio::DB::Query::HIVQuery.3p > @man man/man3p/Bio::DB::Query::WebQuery.3p > @man man/man3p/Bio::DB::QueryI.3p > @man man/man3p/Bio::DB::RandomAccessI.3p > -@man man/man3p/Bio::DB::RefSeq.3p > @man man/man3p/Bio::DB::ReferenceI.3p > @man man/man3p/Bio::DB::Registry.3p > -@man man/man3p/Bio::DB::SeqFeature.3p > -@man man/man3p/Bio::DB::SeqFeature::NormalizedFeature.3p > -@man man/man3p/Bio::DB::SeqFeature::NormalizedFeatureI.3p > -@man man/man3p/Bio::DB::SeqFeature::NormalizedTableFeatureI.3p > -@man man/man3p/Bio::DB::SeqFeature::Segment.3p > -@man man/man3p/Bio::DB::SeqFeature::Store.3p > -@man man/man3p/Bio::DB::SeqFeature::Store::DBI::Iterator.3p > -@man man/man3p/Bio::DB::SeqFeature::Store::DBI::Pg.3p > -@man man/man3p/Bio::DB::SeqFeature::Store::DBI::SQLite.3p > -@man man/man3p/Bio::DB::SeqFeature::Store::DBI::mysql.3p > -@man man/man3p/Bio::DB::SeqFeature::Store::FeatureFileLoader.3p > -@man man/man3p/Bio::DB::SeqFeature::Store::GFF2Loader.3p > -@man man/man3p/Bio::DB::SeqFeature::Store::GFF3Loader.3p > -@man man/man3p/Bio::DB::SeqFeature::Store::LoadHelper.3p > -@man man/man3p/Bio::DB::SeqFeature::Store::Loader.3p > -@man man/man3p/Bio::DB::SeqFeature::Store::bdb.3p > -@man man/man3p/Bio::DB::SeqFeature::Store::berkeleydb.3p > -@man man/man3p/Bio::DB::SeqFeature::Store::berkeleydb3.3p > -@man man/man3p/Bio::DB::SeqFeature::Store::memory.3p > -@man man/man3p/Bio::DB::SeqHound.3p > @man man/man3p/Bio::DB::SeqI.3p > -@man man/man3p/Bio::DB::SeqVersion.3p > -@man man/man3p/Bio::DB::SeqVersion::gi.3p > -@man man/man3p/Bio::DB::SwissProt.3p > -@man man/man3p/Bio::DB::TFBS.3p > -@man man/man3p/Bio::DB::TFBS::transfac_pro.3p > @man man/man3p/Bio::DB::Taxonomy.3p > -@man man/man3p/Bio::DB::Taxonomy::entrez.3p > @man man/man3p/Bio::DB::Taxonomy::flatfile.3p > @man man/man3p/Bio::DB::Taxonomy::greengenes.3p > @man man/man3p/Bio::DB::Taxonomy::list.3p > @man man/man3p/Bio::DB::Taxonomy::silva.3p > -@man man/man3p/Bio::DB::Universal.3p > @man man/man3p/Bio::DB::UpdateableSeqI.3p > @man man/man3p/Bio::DB::WebDBSeqI.3p > @man man/man3p/Bio::DBLinkContainerI.3p > @@ -1274,7 +700,6 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Das::SegmentI.3p > @man man/man3p/Bio::DasI.3p > @man man/man3p/Bio::DescribableI.3p > -@man man/man3p/Bio::Draw::Pictogram.3p > @man man/man3p/Bio::Event::EventGeneratorI.3p > @man man/man3p/Bio::Event::EventHandlerI.3p > @man man/man3p/Bio::Factory::AnalysisI.3p > @@ -1282,7 +707,6 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Factory::DriverFactory.3p > @man man/man3p/Bio::Factory::FTLocationFactory.3p > @man man/man3p/Bio::Factory::LocationFactoryI.3p > -@man man/man3p/Bio::Factory::MapFactoryI.3p > @man man/man3p/Bio::Factory::ObjectBuilderI.3p > @man man/man3p/Bio::Factory::ObjectFactory.3p > @man man/man3p/Bio::Factory::ObjectFactoryI.3p > @@ -1304,29 +728,9 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Index::Fasta.3p > @man man/man3p/Bio::Index::Fastq.3p > @man man/man3p/Bio::Index::GenBank.3p > -@man man/man3p/Bio::Index::Hmmer.3p > @man man/man3p/Bio::Index::Qual.3p > -@man man/man3p/Bio::Index::Stockholm.3p > @man man/man3p/Bio::Index::SwissPfam.3p > @man man/man3p/Bio::Index::Swissprot.3p > -@man man/man3p/Bio::LiveSeq::AARange.3p > -@man man/man3p/Bio::LiveSeq::Chain.3p > -@man man/man3p/Bio::LiveSeq::ChainI.3p > -@man man/man3p/Bio::LiveSeq::DNA.3p > -@man man/man3p/Bio::LiveSeq::Exon.3p > -@man man/man3p/Bio::LiveSeq::Gene.3p > -@man man/man3p/Bio::LiveSeq::IO::BioPerl.3p > -@man man/man3p/Bio::LiveSeq::IO::Loader.3p > -@man man/man3p/Bio::LiveSeq::Intron.3p > -@man man/man3p/Bio::LiveSeq::Mutation.3p > -@man man/man3p/Bio::LiveSeq::Mutator.3p > -@man man/man3p/Bio::LiveSeq::Prim_Transcript.3p > -@man man/man3p/Bio::LiveSeq::Range.3p > -@man man/man3p/Bio::LiveSeq::Repeat_Region.3p > -@man man/man3p/Bio::LiveSeq::Repeat_Unit.3p > -@man man/man3p/Bio::LiveSeq::SeqI.3p > -@man man/man3p/Bio::LiveSeq::Transcript.3p > -@man man/man3p/Bio::LiveSeq::Translation.3p > @man man/man3p/Bio::LocatableSeq.3p > @man man/man3p/Bio::Location::Atomic.3p > @man man/man3p/Bio::Location::AvWithinCoordPolicy.3p > @@ -1339,41 +743,6 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Location::SplitLocationI.3p > @man man/man3p/Bio::Location::WidestCoordPolicy.3p > @man man/man3p/Bio::LocationI.3p > -@man man/man3p/Bio::Map::Clone.3p > -@man man/man3p/Bio::Map::Contig.3p > -@man man/man3p/Bio::Map::CytoMap.3p > -@man man/man3p/Bio::Map::CytoMarker.3p > -@man man/man3p/Bio::Map::CytoPosition.3p > -@man man/man3p/Bio::Map::EntityI.3p > -@man man/man3p/Bio::Map::FPCMarker.3p > -@man man/man3p/Bio::Map::Gene.3p > -@man man/man3p/Bio::Map::GeneMap.3p > -@man man/man3p/Bio::Map::GenePosition.3p > -@man man/man3p/Bio::Map::GeneRelative.3p > -@man man/man3p/Bio::Map::LinkageMap.3p > -@man man/man3p/Bio::Map::LinkagePosition.3p > -@man man/man3p/Bio::Map::MapI.3p > -@man man/man3p/Bio::Map::Mappable.3p > -@man man/man3p/Bio::Map::MappableI.3p > -@man man/man3p/Bio::Map::Marker.3p > -@man man/man3p/Bio::Map::MarkerI.3p > -@man man/man3p/Bio::Map::Microsatellite.3p > -@man man/man3p/Bio::Map::OrderedPosition.3p > -@man man/man3p/Bio::Map::OrderedPositionWithDistance.3p > -@man man/man3p/Bio::Map::Physical.3p > -@man man/man3p/Bio::Map::Position.3p > -@man man/man3p/Bio::Map::PositionHandler.3p > -@man man/man3p/Bio::Map::PositionHandlerI.3p > -@man man/man3p/Bio::Map::PositionI.3p > -@man man/man3p/Bio::Map::PositionWithSequence.3p > -@man man/man3p/Bio::Map::Prediction.3p > -@man man/man3p/Bio::Map::Relative.3p > -@man man/man3p/Bio::Map::RelativeI.3p > -@man man/man3p/Bio::Map::SimpleMap.3p > -@man man/man3p/Bio::Map::TranscriptionFactor.3p > -@man man/man3p/Bio::MapIO.3p > -@man man/man3p/Bio::MapIO::fpc.3p > -@man man/man3p/Bio::MapIO::mapmaker.3p > @man man/man3p/Bio::Matrix::Generic.3p > @man man/man3p/Bio::Matrix::IO.3p > @man man/man3p/Bio::Matrix::IO::mlagan.3p > @@ -1399,9 +768,6 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Matrix::PSM::SiteMatrixI.3p > @man man/man3p/Bio::Matrix::PhylipDist.3p > @man man/man3p/Bio::Matrix::Scoring.3p > -@man man/man3p/Bio::MolEvol::CodonModel.3p > -@man man/man3p/Bio::Nexml::Factory.3p > -@man man/man3p/Bio::NexmlIO.3p > @man man/man3p/Bio::Ontology::DocumentRegistry.3p > @man man/man3p/Bio::Ontology::GOterm.3p > @man man/man3p/Bio::Ontology::InterProTerm.3p > @@ -1433,64 +799,11 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::OntologyIO::simplehierarchy.3p > @man man/man3p/Bio::OntologyIO::soflat.3p > @man man/man3p/Bio::ParameterBaseI.3p > -@man man/man3p/Bio::Perl.3p > -@man man/man3p/Bio::Phenotype::Correlate.3p > -@man man/man3p/Bio::Phenotype::MeSH::Term.3p > -@man man/man3p/Bio::Phenotype::MeSH::Twig.3p > -@man man/man3p/Bio::Phenotype::Measure.3p > -@man man/man3p/Bio::Phenotype::OMIM::MiniMIMentry.3p > -@man man/man3p/Bio::Phenotype::OMIM::OMIMentry.3p > -@man man/man3p/Bio::Phenotype::OMIM::OMIMentryAllelicVariant.3p > -@man man/man3p/Bio::Phenotype::OMIM::OMIMparser.3p > -@man man/man3p/Bio::Phenotype::Phenotype.3p > -@man man/man3p/Bio::Phenotype::PhenotypeI.3p > -@man man/man3p/Bio::PhyloNetwork.3p > -@man man/man3p/Bio::PhyloNetwork::Factory.3p > -@man man/man3p/Bio::PhyloNetwork::FactoryX.3p > -@man man/man3p/Bio::PhyloNetwork::GraphViz.3p > -@man man/man3p/Bio::PhyloNetwork::RandomFactory.3p > -@man man/man3p/Bio::PhyloNetwork::TreeFactory.3p > -@man man/man3p/Bio::PhyloNetwork::TreeFactoryMulti.3p > -@man man/man3p/Bio::PhyloNetwork::TreeFactoryX.3p > -@man man/man3p/Bio::PhyloNetwork::muVector.3p > -@man man/man3p/Bio::PopGen::Genotype.3p > -@man man/man3p/Bio::PopGen::GenotypeI.3p > -@man man/man3p/Bio::PopGen::HtSNP.3p > -@man man/man3p/Bio::PopGen::IO.3p > -@man man/man3p/Bio::PopGen::IO::csv.3p > -@man man/man3p/Bio::PopGen::IO::hapmap.3p > -@man man/man3p/Bio::PopGen::IO::phase.3p > -@man man/man3p/Bio::PopGen::IO::prettybase.3p > -@man man/man3p/Bio::PopGen::Individual.3p > -@man man/man3p/Bio::PopGen::IndividualI.3p > -@man man/man3p/Bio::PopGen::Marker.3p > -@man man/man3p/Bio::PopGen::MarkerI.3p > -@man man/man3p/Bio::PopGen::PopStats.3p > -@man man/man3p/Bio::PopGen::Population.3p > -@man man/man3p/Bio::PopGen::PopulationI.3p > -@man man/man3p/Bio::PopGen::Simulation::Coalescent.3p > -@man man/man3p/Bio::PopGen::Simulation::GeneticDrift.3p > -@man man/man3p/Bio::PopGen::Statistics.3p > -@man man/man3p/Bio::PopGen::TagHaplotype.3p > -@man man/man3p/Bio::PopGen::Utilities.3p > @man man/man3p/Bio::PrimarySeq.3p > @man man/man3p/Bio::PrimarySeqI.3p > @man man/man3p/Bio::PullParserI.3p > @man man/man3p/Bio::Range.3p > @man man/man3p/Bio::RangeI.3p > -@man man/man3p/Bio::Restriction::Analysis.3p > -@man man/man3p/Bio::Restriction::Enzyme.3p > -@man man/man3p/Bio::Restriction::Enzyme::MultiCut.3p > -@man man/man3p/Bio::Restriction::Enzyme::MultiSite.3p > -@man man/man3p/Bio::Restriction::EnzymeCollection.3p > -@man man/man3p/Bio::Restriction::EnzymeI.3p > -@man man/man3p/Bio::Restriction::IO.3p > -@man man/man3p/Bio::Restriction::IO::bairoch.3p > -@man man/man3p/Bio::Restriction::IO::base.3p > -@man man/man3p/Bio::Restriction::IO::itype2.3p > -@man man/man3p/Bio::Restriction::IO::prototype.3p > -@man man/man3p/Bio::Restriction::IO::withrefm.3p > -@man man/man3p/Bio::Root::Build.3p > @man man/man3p/Bio::Root::Exception.3p > @man man/man3p/Bio::Root::HTTPget.3p > @man man/man3p/Bio::Root::IO.3p > @@ -1498,6 +811,7 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Root::RootI.3p > @man man/man3p/Bio::Root::Storable.3p > @man man/man3p/Bio::Root::Test.3p > +@man man/man3p/Bio::Root::TestObject.3p > @man man/man3p/Bio::Root::Utilities.3p > @man man/man3p/Bio::Root::Version.3p > @man man/man3p/Bio::Search::BlastStatistics.3p > @@ -1509,10 +823,8 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Search::HSP::BlastPullHSP.3p > @man man/man3p/Bio::Search::HSP::FastaHSP.3p > @man man/man3p/Bio::Search::HSP::GenericHSP.3p > -@man man/man3p/Bio::Search::HSP::HMMERHSP.3p > @man man/man3p/Bio::Search::HSP::HSPFactory.3p > @man man/man3p/Bio::Search::HSP::HSPI.3p > -@man man/man3p/Bio::Search::HSP::HmmpfamHSP.3p > @man man/man3p/Bio::Search::HSP::ModelHSP.3p > @man man/man3p/Bio::Search::HSP::PSLHSP.3p > @man man/man3p/Bio::Search::HSP::PsiBlastHSP.3p > @@ -1522,14 +834,11 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Search::Hit::BlastPullHit.3p > @man man/man3p/Bio::Search::Hit::Fasta.3p > @man man/man3p/Bio::Search::Hit::GenericHit.3p > -@man man/man3p/Bio::Search::Hit::HMMERHit.3p > @man man/man3p/Bio::Search::Hit::HitFactory.3p > @man man/man3p/Bio::Search::Hit::HitI.3p > -@man man/man3p/Bio::Search::Hit::HmmpfamHit.3p > @man man/man3p/Bio::Search::Hit::ModelHit.3p > @man man/man3p/Bio::Search::Hit::PsiBlastHit.3p > @man man/man3p/Bio::Search::Hit::PullHitI.3p > -@man man/man3p/Bio::Search::Hit::hmmer3Hit.3p > @man man/man3p/Bio::Search::Iteration::GenericIteration.3p > @man man/man3p/Bio::Search::Iteration::IterationI.3p > @man man/man3p/Bio::Search::Processor.3p > @@ -1537,48 +846,37 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Search::Result::BlastResult.3p > @man man/man3p/Bio::Search::Result::CrossMatchResult.3p > @man man/man3p/Bio::Search::Result::GenericResult.3p > -@man man/man3p/Bio::Search::Result::HMMERResult.3p > -@man man/man3p/Bio::Search::Result::HmmpfamResult.3p > +@man man/man3p/Bio::Search::Result::INFERNALResult.3p > @man man/man3p/Bio::Search::Result::PullResultI.3p > @man man/man3p/Bio::Search::Result::ResultFactory.3p > @man man/man3p/Bio::Search::Result::ResultI.3p > @man man/man3p/Bio::Search::Result::WABAResult.3p > -@man man/man3p/Bio::Search::Result::hmmer3Result.3p > @man man/man3p/Bio::Search::SearchUtils.3p > @man man/man3p/Bio::Search::StatisticsI.3p > @man man/man3p/Bio::Search::Tiling::MapTileUtils.3p > @man man/man3p/Bio::Search::Tiling::MapTiling.3p > @man man/man3p/Bio::Search::Tiling::TilingI.3p > -@man man/man3p/Bio::SearchDist.3p > @man man/man3p/Bio::SearchIO.3p > @man man/man3p/Bio::SearchIO::EventHandlerI.3p > @man man/man3p/Bio::SearchIO::FastHitEventBuilder.3p > @man man/man3p/Bio::SearchIO::IteratedSearchResultEventBuilder.3p > @man man/man3p/Bio::SearchIO::SearchResultEventBuilder.3p > @man man/man3p/Bio::SearchIO::SearchWriterI.3p > -@man man/man3p/Bio::SearchIO::Writer::BSMLResultWriter.3p > @man man/man3p/Bio::SearchIO::Writer::GbrowseGFF.3p > @man man/man3p/Bio::SearchIO::Writer::HSPTableWriter.3p > @man man/man3p/Bio::SearchIO::Writer::HTMLResultWriter.3p > @man man/man3p/Bio::SearchIO::Writer::HitTableWriter.3p > @man man/man3p/Bio::SearchIO::Writer::ResultTableWriter.3p > @man man/man3p/Bio::SearchIO::Writer::TextResultWriter.3p > -@man man/man3p/Bio::SearchIO::XML::BlastHandler.3p > -@man man/man3p/Bio::SearchIO::XML::PsiBlastHandler.3p > @man man/man3p/Bio::SearchIO::axt.3p > @man man/man3p/Bio::SearchIO::blast.3p > @man man/man3p/Bio::SearchIO::blast_pull.3p > @man man/man3p/Bio::SearchIO::blasttable.3p > -@man man/man3p/Bio::SearchIO::blastxml.3p > @man man/man3p/Bio::SearchIO::cross_match.3p > @man man/man3p/Bio::SearchIO::erpin.3p > @man man/man3p/Bio::SearchIO::exonerate.3p > @man man/man3p/Bio::SearchIO::fasta.3p > @man man/man3p/Bio::SearchIO::gmap_f9.3p > -@man man/man3p/Bio::SearchIO::hmmer.3p > -@man man/man3p/Bio::SearchIO::hmmer2.3p > -@man man/man3p/Bio::SearchIO::hmmer3.3p > -@man man/man3p/Bio::SearchIO::hmmer_pull.3p > @man man/man3p/Bio::SearchIO::infernal.3p > @man man/man3p/Bio::SearchIO::megablast.3p > @man man/man3p/Bio::SearchIO::psl.3p > @@ -1605,14 +903,10 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Seq::SeqBuilder.3p > @man man/man3p/Bio::Seq::SeqFactory.3p > @man man/man3p/Bio::Seq::SeqFastaSpeedFactory.3p > -@man man/man3p/Bio::Seq::SeqWithQuality.3p > @man man/man3p/Bio::Seq::SequenceTrace.3p > @man man/man3p/Bio::Seq::SimulatedRead.3p > @man man/man3p/Bio::Seq::TraceI.3p > @man man/man3p/Bio::SeqAnalysisParserI.3p > -@man man/man3p/Bio::SeqEvolution::DNAPoint.3p > -@man man/man3p/Bio::SeqEvolution::EvolutionI.3p > -@man man/man3p/Bio::SeqEvolution::Factory.3p > @man man/man3p/Bio::SeqFeature::Amplicon.3p > @man man/man3p/Bio::SeqFeature::AnnotationAdaptor.3p > @man man/man3p/Bio::SeqFeature::Collection.3p > @@ -1634,8 +928,6 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::SeqFeature::Lite.3p > @man man/man3p/Bio::SeqFeature::PositionProxy.3p > @man man/man3p/Bio::SeqFeature::Primer.3p > -@man man/man3p/Bio::SeqFeature::SiRNA::Oligo.3p > -@man man/man3p/Bio::SeqFeature::SiRNA::Pair.3p > @man man/man3p/Bio::SeqFeature::Similarity.3p > @man man/man3p/Bio::SeqFeature::SimilarityPair.3p > @man man/man3p/Bio::SeqFeature::SubSeq.3p > @@ -1650,25 +942,14 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::SeqIO::FTHelper.3p > @man man/man3p/Bio::SeqIO::Handler::GenericRichSeqHandler.3p > @man man/man3p/Bio::SeqIO::MultiFile.3p > -@man man/man3p/Bio::SeqIO::abi.3p > @man man/man3p/Bio::SeqIO::ace.3p > -@man man/man3p/Bio::SeqIO::agave.3p > -@man man/man3p/Bio::SeqIO::alf.3p > @man man/man3p/Bio::SeqIO::asciitree.3p > @man man/man3p/Bio::SeqIO::bsml.3p > @man man/man3p/Bio::SeqIO::bsml_sax.3p > -@man man/man3p/Bio::SeqIO::chadoxml.3p > -@man man/man3p/Bio::SeqIO::chaos.3p > -@man man/man3p/Bio::SeqIO::chaosxml.3p > -@man man/man3p/Bio::SeqIO::ctf.3p > @man man/man3p/Bio::SeqIO::embl.3p > @man man/man3p/Bio::SeqIO::embldriver.3p > -@man man/man3p/Bio::SeqIO::entrezgene.3p > -@man man/man3p/Bio::SeqIO::excel.3p > -@man man/man3p/Bio::SeqIO::exp.3p > @man man/man3p/Bio::SeqIO::fasta.3p > @man man/man3p/Bio::SeqIO::fastq.3p > -@man man/man3p/Bio::SeqIO::flybase_chadoxml.3p > @man man/man3p/Bio::SeqIO::game.3p > @man man/man3p/Bio::SeqIO::game::featHandler.3p > @man man/man3p/Bio::SeqIO::game::gameHandler.3p > @@ -1682,20 +963,16 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::SeqIO::interpro.3p > @man man/man3p/Bio::SeqIO::kegg.3p > @man man/man3p/Bio::SeqIO::largefasta.3p > -@man man/man3p/Bio::SeqIO::lasergene.3p > @man man/man3p/Bio::SeqIO::locuslink.3p > @man man/man3p/Bio::SeqIO::mbsout.3p > @man man/man3p/Bio::SeqIO::metafasta.3p > @man man/man3p/Bio::SeqIO::msout.3p > -@man man/man3p/Bio::SeqIO::nexml.3p > @man man/man3p/Bio::SeqIO::phd.3p > @man man/man3p/Bio::SeqIO::pir.3p > -@man man/man3p/Bio::SeqIO::pln.3p > @man man/man3p/Bio::SeqIO::qual.3p > @man man/man3p/Bio::SeqIO::raw.3p > @man man/man3p/Bio::SeqIO::scf.3p > @man man/man3p/Bio::SeqIO::seqxml.3p > -@man man/man3p/Bio::SeqIO::strider.3p > @man man/man3p/Bio::SeqIO::swiss.3p > @man man/man3p/Bio::SeqIO::swissdriver.3p > @man man/man3p/Bio::SeqIO::tab.3p > @@ -1704,46 +981,14 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::SeqIO::tigrxml.3p > @man man/man3p/Bio::SeqIO::tinyseq.3p > @man man/man3p/Bio::SeqIO::tinyseq::tinyseqHandler.3p > -@man man/man3p/Bio::SeqIO::ztr.3p > @man man/man3p/Bio::SeqUtils.3p > @man man/man3p/Bio::SimpleAlign.3p > @man man/man3p/Bio::SimpleAnalysisI.3p > @man man/man3p/Bio::Species.3p > -@man man/man3p/Bio::Structure::Atom.3p > -@man man/man3p/Bio::Structure::Chain.3p > -@man man/man3p/Bio::Structure::Entry.3p > -@man man/man3p/Bio::Structure::IO.3p > -@man man/man3p/Bio::Structure::IO::pdb.3p > -@man man/man3p/Bio::Structure::Model.3p > -@man man/man3p/Bio::Structure::Residue.3p > -@man man/man3p/Bio::Structure::SecStr::DSSP::Res.3p > -@man man/man3p/Bio::Structure::SecStr::STRIDE::Res.3p > -@man man/man3p/Bio::Structure::StructureI.3p > -@man man/man3p/Bio::Symbol::Alphabet.3p > -@man man/man3p/Bio::Symbol::AlphabetI.3p > -@man man/man3p/Bio::Symbol::DNAAlphabet.3p > -@man man/man3p/Bio::Symbol::ProteinAlphabet.3p > -@man man/man3p/Bio::Symbol::Symbol.3p > -@man man/man3p/Bio::Symbol::SymbolI.3p > @man man/man3p/Bio::Taxon.3p > -@man man/man3p/Bio::Taxonomy.3p > -@man man/man3p/Bio::Taxonomy::FactoryI.3p > -@man man/man3p/Bio::Taxonomy::Node.3p > -@man man/man3p/Bio::Taxonomy::Taxon.3p > -@man man/man3p/Bio::Taxonomy::Tree.3p > -@man man/man3p/Bio::Tools::AlignFactory.3p > @man man/man3p/Bio::Tools::Alignment::Consed.3p > @man man/man3p/Bio::Tools::Alignment::Trim.3p > @man man/man3p/Bio::Tools::AmpliconSearch.3p > -@man man/man3p/Bio::Tools::Analysis::DNA::ESEfinder.3p > -@man man/man3p/Bio::Tools::Analysis::Protein::Domcut.3p > -@man man/man3p/Bio::Tools::Analysis::Protein::ELM.3p > -@man man/man3p/Bio::Tools::Analysis::Protein::GOR4.3p > -@man man/man3p/Bio::Tools::Analysis::Protein::HNN.3p > -@man man/man3p/Bio::Tools::Analysis::Protein::Mitoprot.3p > -@man man/man3p/Bio::Tools::Analysis::Protein::NetPhos.3p > -@man man/man3p/Bio::Tools::Analysis::Protein::Scansite.3p > -@man man/man3p/Bio::Tools::Analysis::Protein::Sopma.3p > @man man/man3p/Bio::Tools::Analysis::SimpleAnalysisBase.3p > @man man/man3p/Bio::Tools::AnalysisResult.3p > @man man/man3p/Bio::Tools::Blat.3p > @@ -1752,14 +997,12 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Tools::ECnumber.3p > @man man/man3p/Bio::Tools::EMBOSS::Palindrome.3p > @man man/man3p/Bio::Tools::EPCR.3p > -@man man/man3p/Bio::Tools::ERPIN.3p > @man man/man3p/Bio::Tools::ESTScan.3p > @man man/man3p/Bio::Tools::Eponine.3p > @man man/man3p/Bio::Tools::Est2Genome.3p > @man man/man3p/Bio::Tools::Fgenesh.3p > @man man/man3p/Bio::Tools::FootPrinter.3p > @man man/man3p/Bio::Tools::GFF.3p > -@man man/man3p/Bio::Tools::Gel.3p > @man man/man3p/Bio::Tools::Geneid.3p > @man man/man3p/Bio::Tools::Genemark.3p > @man man/man3p/Bio::Tools::Genewise.3p > @@ -1768,24 +1011,14 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Tools::Glimmer.3p > @man man/man3p/Bio::Tools::Grail.3p > @man man/man3p/Bio::Tools::GuessSeqFormat.3p > -@man man/man3p/Bio::Tools::HMMER::Domain.3p > -@man man/man3p/Bio::Tools::HMMER::Results.3p > -@man man/man3p/Bio::Tools::HMMER::Set.3p > -@man man/man3p/Bio::Tools::Hmmpfam.3p > @man man/man3p/Bio::Tools::IUPAC.3p > -@man man/man3p/Bio::Tools::Infernal.3p > @man man/man3p/Bio::Tools::Lucy.3p > @man man/man3p/Bio::Tools::MZEF.3p > @man man/man3p/Bio::Tools::Match.3p > @man man/man3p/Bio::Tools::OddCodes.3p > @man man/man3p/Bio::Tools::Phylo::Gerp.3p > -@man man/man3p/Bio::Tools::Phylo::Gumby.3p > @man man/man3p/Bio::Tools::Phylo::Molphy.3p > @man man/man3p/Bio::Tools::Phylo::Molphy::Result.3p > -@man man/man3p/Bio::Tools::Phylo::PAML.3p > -@man man/man3p/Bio::Tools::Phylo::PAML::Codeml.3p > -@man man/man3p/Bio::Tools::Phylo::PAML::ModelResult.3p > -@man man/man3p/Bio::Tools::Phylo::PAML::Result.3p > @man man/man3p/Bio::Tools::Phylo::Phylip::ProtDist.3p > @man man/man3p/Bio::Tools::Prediction::Exon.3p > @man man/man3p/Bio::Tools::Prediction::Gene.3p > @@ -1798,18 +1031,15 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Tools::Profile.3p > @man man/man3p/Bio::Tools::Promoterwise.3p > @man man/man3p/Bio::Tools::PrositeScan.3p > -@man man/man3p/Bio::Tools::Protparam.3p > @man man/man3p/Bio::Tools::Pseudowise.3p > @man man/man3p/Bio::Tools::QRNA.3p > -@man man/man3p/Bio::Tools::RNAMotif.3p > @man man/man3p/Bio::Tools::RandomDistFunctions.3p > @man man/man3p/Bio::Tools::RepeatMasker.3p > +@man man/man3p/Bio::Tools::Run::Analysis.3p > +@man man/man3p/Bio::Tools::Run::AnalysisFactory.3p > @man man/man3p/Bio::Tools::Run::GenericParameters.3p > @man man/man3p/Bio::Tools::Run::ParametersI.3p > -@man man/man3p/Bio::Tools::Run::RemoteBlast.3p > -@man man/man3p/Bio::Tools::Run::StandAloneBlast.3p > -@man man/man3p/Bio::Tools::Run::StandAloneNCBIBlast.3p > -@man man/man3p/Bio::Tools::Run::StandAloneWUBlast.3p > +@man man/man3p/Bio::Tools::Run::Phylo::PhyloBase.3p > @man man/man3p/Bio::Tools::Run::WrapperBase.3p > @man man/man3p/Bio::Tools::Run::WrapperBase::CommandExts.3p > @man man/man3p/Bio::Tools::Seg.3p > @@ -1817,9 +1047,6 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Tools::SeqPattern::Backtranslate.3p > @man man/man3p/Bio::Tools::SeqStats.3p > @man man/man3p/Bio::Tools::SeqWords.3p > -@man man/man3p/Bio::Tools::SiRNA.3p > -@man man/man3p/Bio::Tools::SiRNA::Ruleset::saigo.3p > -@man man/man3p/Bio::Tools::SiRNA::Ruleset::tuschl.3p > @man man/man3p/Bio::Tools::Sigcleave.3p > @man man/man3p/Bio::Tools::Signalp.3p > @man man/man3p/Bio::Tools::Signalp::ExtendedSignalp.3p > @@ -1830,17 +1057,13 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::Tools::TandemRepeatsFinder.3p > @man man/man3p/Bio::Tools::TargetP.3p > @man man/man3p/Bio::Tools::Tmhmm.3p > -@man man/man3p/Bio::Tools::dpAlign.3p > @man man/man3p/Bio::Tools::ipcress.3p > @man man/man3p/Bio::Tools::isPcr.3p > @man man/man3p/Bio::Tools::pICalculator.3p > -@man man/man3p/Bio::Tools::pSW.3p > @man man/man3p/Bio::Tools::tRNAscanSE.3p > -@man man/man3p/Bio::Tree::AlleleNode.3p > @man man/man3p/Bio::Tree::AnnotatableNode.3p > @man man/man3p/Bio::Tree::Compatible.3p > @man man/man3p/Bio::Tree::DistanceFactory.3p > -@man man/man3p/Bio::Tree::Draw::Cladogram.3p > @man man/man3p/Bio::Tree::Node.3p > @man man/man3p/Bio::Tree::NodeI.3p > @man man/man3p/Bio::Tree::NodeNHX.3p > @@ -1855,26 +1078,14 @@ ${P5SITE}/Bio/WebAgent.pm > @man man/man3p/Bio::TreeIO::cluster.3p > @man man/man3p/Bio::TreeIO::lintree.3p > @man man/man3p/Bio::TreeIO::newick.3p > -@man man/man3p/Bio::TreeIO::nexml.3p > @man man/man3p/Bio::TreeIO::nexus.3p > @man man/man3p/Bio::TreeIO::nhx.3p > @man man/man3p/Bio::TreeIO::pag.3p > @man man/man3p/Bio::TreeIO::phyloxml.3p > -@man man/man3p/Bio::TreeIO::svggraph.3p > @man man/man3p/Bio::TreeIO::tabtree.3p > @man man/man3p/Bio::UpdateableSeqI.3p > -@man man/man3p/Bio::Variation::AAChange.3p > -@man man/man3p/Bio::Variation::AAReverseMutate.3p > -@man man/man3p/Bio::Variation::Allele.3p > -@man man/man3p/Bio::Variation::DNAMutation.3p > -@man man/man3p/Bio::Variation::IO.3p > -@man man/man3p/Bio::Variation::IO::flat.3p > -@man man/man3p/Bio::Variation::IO::xml.3p > -@man man/man3p/Bio::Variation::RNAChange.3p > -@man man/man3p/Bio::Variation::SNP.3p > -@man man/man3p/Bio::Variation::SeqDiff.3p > -@man man/man3p/Bio::Variation::VariantI.3p > @man man/man3p/Bio::WebAgent.3p > +@man man/man3p/BioPerl.3p > share/examples/bioperl/ > share/examples/bioperl/Bio-DB-GFF/ > share/examples/bioperl/Bio-DB-GFF/load_ucsc.pl > @@ -1882,30 +1093,20 @@ share/examples/bioperl/align/ > share/examples/bioperl/align/FastAlign.pl > share/examples/bioperl/align/align_on_codons.pl > share/examples/bioperl/align/aligntutorial.pl > -share/examples/bioperl/align/clustalw.pl > share/examples/bioperl/align/simplealign.pl > -share/examples/bioperl/bioperl.pl > -share/examples/bioperl/cluster/ > -share/examples/bioperl/cluster/dbsnp.pl > +share/examples/bioperl/classify_hits_kingdom > share/examples/bioperl/contributed/ > share/examples/bioperl/contributed/nmrpdb_parse.pl > share/examples/bioperl/contributed/prosite2perl.pl > share/examples/bioperl/contributed/rebase2list.pl > share/examples/bioperl/db/ > -share/examples/bioperl/db/dbfetch > share/examples/bioperl/db/est_tissue_query.pl > -share/examples/bioperl/db/gb2features.pl > -share/examples/bioperl/db/getGenBank.pl > share/examples/bioperl/db/get_seqs.pl > share/examples/bioperl/db/rfetch.pl > share/examples/bioperl/db/use_registry.pl > share/examples/bioperl/generate_random_seq.pl > -share/examples/bioperl/liveseq/ > -share/examples/bioperl/liveseq/change_gene.pl > share/examples/bioperl/longorf.pl > share/examples/bioperl/make_primers.pl > -share/examples/bioperl/popgen/ > -share/examples/bioperl/popgen/parse_calc_stats.pl > share/examples/bioperl/quality/ > share/examples/bioperl/quality/svgtrace.pl > share/examples/bioperl/rev_and_trans.pl > @@ -1916,9 +1117,6 @@ share/examples/bioperl/root/exceptions1. > share/examples/bioperl/root/exceptions2.pl > share/examples/bioperl/root/exceptions3.pl > share/examples/bioperl/root/exceptions4.pl > -share/examples/bioperl/root/lib/ > -share/examples/bioperl/root/lib/TestInterface.pm > -share/examples/bioperl/root/lib/TestObject.pm > share/examples/bioperl/searchio/ > share/examples/bioperl/searchio/blast_example.pl > share/examples/bioperl/searchio/custom_writer.pl > @@ -1931,12 +1129,6 @@ share/examples/bioperl/searchio/rawwrite > share/examples/bioperl/searchio/resultwriter.pl > share/examples/bioperl/searchio/waba2gff.pl > share/examples/bioperl/searchio/waba2gff3.pl > -share/examples/bioperl/sirna/ > -share/examples/bioperl/sirna/TAG > -share/examples/bioperl/sirna/rnai_finder.cgi > -share/examples/bioperl/structure/ > -share/examples/bioperl/structure/structure-io.pl > -share/examples/bioperl/subsequence.cgi > share/examples/bioperl/tk/ > share/examples/bioperl/tk/gsequence.pl > share/examples/bioperl/tk/hitdisplay.pl > @@ -1945,7 +1137,6 @@ share/examples/bioperl/tools/extract_gen > share/examples/bioperl/tools/gb_to_gff.pl > share/examples/bioperl/tools/gff2ps.pl > share/examples/bioperl/tools/parse_codeml.pl > -share/examples/bioperl/tools/psw.pl > share/examples/bioperl/tools/reverse-translate.pl > share/examples/bioperl/tools/run_genscan.pl > share/examples/bioperl/tools/run_primer3.pl > Index: p5-Bio-ASN1-EntrezGene/Makefile > =================================================================== > RCS file: /cvs/ports/biology/p5-Bio-ASN1-EntrezGene/Makefile,v > retrieving revision 1.13 > diff -u -p -r1.13 Makefile > --- p5-Bio-ASN1-EntrezGene/Makefile 9 Aug 2019 16:03:10 -0000 1.13 > +++ p5-Bio-ASN1-EntrezGene/Makefile 20 Aug 2020 10:11:28 -0000 > @@ -2,22 +2,18 @@ > > COMMENT = regular expression-based parser for NCBI Entrez Gene > > -M = 1.10-withoutworldwriteables > -DISTNAME = Bio-ASN1-EntrezGene-${M} > -PKGNAME = p5-Bio-ASN1-EntrezGene-${M:S/-withoutworldwriteables//} > -REVISION = 3 > +DISTNAME = Bio-ASN1-EntrezGene-1.73 > EPOCH = 0 > CATEGORIES = biology > > -# perl > +# Perl > PERMIT_PACKAGE = Yes > > MODULES = cpan > PKG_ARCH = * > -MODCPAN_EXAMPLES= Yes > +MODCPAN_EXAMPLE = Yes > > -WRKDIST = > ${WRKDIR}/Bio-ASN1-EntrezGene-${M:S/-withoutworldwriteables//} > - > -RUN_DEPENDS = biology/bioperl > +RUN_DEPENDS = biology/bioperl>=1.7.7 \ > + biology/p5-Bio-Cluster > > .include <bsd.port.mk> > Index: p5-Bio-ASN1-EntrezGene/distinfo > =================================================================== > RCS file: /cvs/ports/biology/p5-Bio-ASN1-EntrezGene/distinfo,v > retrieving revision 1.3 > diff -u -p -r1.3 distinfo > --- p5-Bio-ASN1-EntrezGene/distinfo 18 Jan 2015 03:12:52 -0000 1.3 > +++ p5-Bio-ASN1-EntrezGene/distinfo 20 Aug 2020 10:11:28 -0000 > @@ -1,2 +1,2 @@ > -SHA256 (Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz) = > mA7WKRIZKqnrcMQfW8F9DksvKfKskMbjBksgnS4O6Ec= > -SIZE (Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz) = 36609 > +SHA256 (Bio-ASN1-EntrezGene-1.73.tar.gz) = > +ed423Bc5cNa0nmOOKhJC2RO39wUJTqht0ofXnn8aks= > +SIZE (Bio-ASN1-EntrezGene-1.73.tar.gz) = 157307 > Index: p5-Bio-ASN1-EntrezGene/patches/patch-lib_Bio_ASN1_EntrezGene_pm > =================================================================== > RCS file: p5-Bio-ASN1-EntrezGene/patches/patch-lib_Bio_ASN1_EntrezGene_pm > diff -N p5-Bio-ASN1-EntrezGene/patches/patch-lib_Bio_ASN1_EntrezGene_pm > --- p5-Bio-ASN1-EntrezGene/patches/patch-lib_Bio_ASN1_EntrezGene_pm 9 Aug > 2019 16:03:10 -0000 1.1 > +++ /dev/null 1 Jan 1970 00:00:00 -0000 > @@ -1,25 +0,0 @@ > -$OpenBSD: patch-lib_Bio_ASN1_EntrezGene_pm,v 1.1 2019/08/09 16:03:10 cwen > Exp $ > - > -Fix unescaped left braces so it does not generate warnings with Perl 5.28 > - > -Index: lib/Bio/ASN1/EntrezGene.pm > ---- lib/Bio/ASN1/EntrezGene.pm.orig > -+++ lib/Bio/ASN1/EntrezGene.pm > -@@ -270,7 +270,7 @@ sub next_seq > - { > - chomp; > - next unless /\S/; > -- my $tmp = (/^\s*Entrezgene ::= ({.*)/si)? $1 : "{" . $_; # get rid of > the 'Entrezgene ::= ' at the beginning of Entrez Gene record > -+ my $tmp = (/^\s*Entrezgene ::= (\{.*)/si)? $1 : "{" . $_; # get rid of > the 'Entrezgene ::= ' at the beginning of Entrez Gene record > - return $self->parse($tmp, $compact, 1); # 1 species no resetting line > number > - } > - } > -@@ -324,7 +324,7 @@ sub _parse > - elsif($data->{$id}) { $data->{$id} = [$data->{$id}, $value] } # > hash value has a second terminal value now! > - else { $data->{$id} = $value } # the first terminal value > - } > -- elsif($self->{input} =~ /\G{/cg) > -+ elsif($self->{input} =~ /\G\{/cg) > - { > - $self->{depth}++; > - push(@{$data->{$id}}, $self->_parse()); > Index: p5-Bio-ASN1-EntrezGene/patches/patch-lib_Bio_ASN1_Sequence_pm > =================================================================== > RCS file: p5-Bio-ASN1-EntrezGene/patches/patch-lib_Bio_ASN1_Sequence_pm > diff -N p5-Bio-ASN1-EntrezGene/patches/patch-lib_Bio_ASN1_Sequence_pm > --- p5-Bio-ASN1-EntrezGene/patches/patch-lib_Bio_ASN1_Sequence_pm 9 Aug > 2019 16:03:10 -0000 1.1 > +++ /dev/null 1 Jan 1970 00:00:00 -0000 > @@ -1,25 +0,0 @@ > -$OpenBSD: patch-lib_Bio_ASN1_Sequence_pm,v 1.1 2019/08/09 16:03:10 cwen Exp $ > - > -Fix unescaped braces as it triggers a warning with Perl 5.28 > - > -Index: lib/Bio/ASN1/Sequence.pm > ---- lib/Bio/ASN1/Sequence.pm.orig > -+++ lib/Bio/ASN1/Sequence.pm > -@@ -256,7 +256,7 @@ sub next_seq > - { > - chomp; > - next unless /\S/; > -- my $tmp = (/^\s*Seq-entry ::= set ({.*)/si)? $1 : "{" . $_; # get rid > of the 'Seq-entry ::= set ' at the beginning of Sequence record > -+ my $tmp = (/^\s*Seq-entry ::= set (\{.*)/si)? $1 : "{" . $_; # get rid > of the 'Seq-entry ::= set ' at the beginning of Sequence record > - return $self->parse($tmp, $compact, 1); # 1 species no resetting line > number > - } > - } > -@@ -317,7 +317,7 @@ sub _parse > - elsif($data->{$id}) { $data->{$id} = [$data->{$id}, $value] } # > hash value has a second terminal value now! > - else { $data->{$id} = $value } # the first terminal value > - } > -- elsif($self->{input} =~ /\G{/cg) > -+ elsif($self->{input} =~ /\G\{/cg) > - { > - $self->{depth}++; > - push(@{$data->{$id}}, $self->_parse()); > Index: p5-Bio-ASN1-EntrezGene/pkg/PLIST > =================================================================== > RCS file: /cvs/ports/biology/p5-Bio-ASN1-EntrezGene/pkg/PLIST,v > retrieving revision 1.3 > diff -u -p -r1.3 PLIST > --- p5-Bio-ASN1-EntrezGene/pkg/PLIST 30 Aug 2010 11:01:07 -0000 1.3 > +++ p5-Bio-ASN1-EntrezGene/pkg/PLIST 20 Aug 2020 10:11:28 -0000 > @@ -1,4 +1,5 @@ > @comment $OpenBSD: PLIST,v 1.3 2010/08/30 11:01:07 jasper Exp $ > +@conflict bioperl-<1.7.* > ${P5SITE}/Bio/ASN1/ > ${P5SITE}/Bio/ASN1/EntrezGene/ > ${P5SITE}/Bio/ASN1/EntrezGene.pm > @@ -6,10 +7,12 @@ ${P5SITE}/Bio/ASN1/EntrezGene/Indexer.pm > ${P5SITE}/Bio/ASN1/Sequence/ > ${P5SITE}/Bio/ASN1/Sequence.pm > ${P5SITE}/Bio/ASN1/Sequence/Indexer.pm > +${P5SITE}/Bio/SeqIO/entrezgene.pm > @man man/man3p/Bio::ASN1::EntrezGene.3p > @man man/man3p/Bio::ASN1::EntrezGene::Indexer.3p > @man man/man3p/Bio::ASN1::Sequence.3p > @man man/man3p/Bio::ASN1::Sequence::Indexer.3p > +@man man/man3p/Bio::SeqIO::entrezgene.3p > share/examples/p5-Bio-ASN1-EntrezGene/ > share/examples/p5-Bio-ASN1-EntrezGene/indexer_test.pl > share/examples/p5-Bio-ASN1-EntrezGene/parse_entrez_gene_example.pl > -- andrew - http://afresh1.com A hacker does for love what others would not do for money.
