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, 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
bioperl_newports.tgz
Description: Binary data
