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authorwen <wen@FreeBSD.org>2009-12-04 19:50:10 +0800
committerwen <wen@FreeBSD.org>2009-12-04 19:50:10 +0800
commitd5fbb7e65730ac030e242136fa6a4d4528cba623 (patch)
tree1398cadfc3210c9ae0d2b43581f0bdc8368d43fd /biology
parentee957b071a74af1d35bf1dc7fccaa1954d79c692 (diff)
downloadfreebsd-ports-graphics-d5fbb7e65730ac030e242136fa6a4d4528cba623.tar.gz
freebsd-ports-graphics-d5fbb7e65730ac030e242136fa6a4d4528cba623.tar.zst
freebsd-ports-graphics-d5fbb7e65730ac030e242136fa6a4d4528cba623.zip
- Update to 1.6.1
Approved by: maintainer (via Email)
Diffstat (limited to 'biology')
-rw-r--r--biology/p5-bioperl/Makefile21
-rw-r--r--biology/p5-bioperl/distinfo6
-rw-r--r--biology/p5-bioperl/files/patch-Bio-Root-Build.pm (renamed from biology/p5-bioperl/files/patch-Build.pm)12
-rw-r--r--biology/p5-bioperl/files/patch-Build.PL19
-rw-r--r--biology/p5-bioperl/pkg-plist1793
5 files changed, 939 insertions, 912 deletions
diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile
index b4c084b61af..9a062710b2d 100644
--- a/biology/p5-bioperl/Makefile
+++ b/biology/p5-bioperl/Makefile
@@ -6,8 +6,7 @@
#
PORTNAME= bioperl
-PORTVERSION= 1.6.0
-PORTREVISION= 1
+PORTVERSION= 1.6.1
CATEGORIES= biology perl5
MASTER_SITES= http://bioperl.org/DIST/ \
CPAN
@@ -64,7 +63,7 @@ BUILD_DEPENDS= ${LOCALBASE}/lib/perl5/${PERL_VERSION}/Text/Wrap.pm:${PORTSDIR}/l
RUN_DEPENDS= ${BUILD_DEPENDS}
-CONFLICTS= p5-bioperl-1.[13579]*
+#CONFLICTS= p5-bioperl-1.[13579]*
PERL_MODBUILD= YES
@@ -80,6 +79,7 @@ MAN1= bp_aacomp.pl.1 \
bp_composite_LD.pl.1 \
bp_dbsplit.pl.1 \
bp_download_query_genbank.pl.1 \
+ bp_einfo.pl.1 \
bp_extract_feature_seq.pl.1 \
bp_fast_load_gff.pl.1 \
bp_fastam9_to_table.pl.1 \
@@ -91,6 +91,7 @@ MAN1= bp_aacomp.pl.1 \
bp_genbank2gff3.pl.1 \
bp_generate_histogram.pl.1 \
bp_heterogeneity_test.pl.1 \
+ bp_hivq.pl.1 \
bp_hmmer_to_table.pl.1 \
bp_index.pl.1 \
bp_load_gff.pl.1 \
@@ -110,6 +111,7 @@ MAN1= bp_aacomp.pl.1 \
bp_process_wormbase.pl.1 \
bp_query_entrez_taxa.pl.1 \
bp_remote_blast.pl.1 \
+ bp_revtrans-motif.pl.1 \
bp_search2BSML.pl.1 \
bp_search2alnblocks.pl.1 \
bp_search2gff.pl.1 \
@@ -227,7 +229,6 @@ MAN3= Bio::Align::AlignI.3 \
Bio::ClusterIO::unigene.3 \
Bio::CodonUsage::IO.3 \
Bio::CodonUsage::Table.3 \
- Bio::ConfigData.3 \
Bio::Coordinate::Chain.3 \
Bio::Coordinate::Collection.3 \
Bio::Coordinate::ExtrapolatingPair.3 \
@@ -338,6 +339,9 @@ MAN3= Bio::Align::AlignI.3 \
Bio::DB::SeqFeature::Store.3 \
Bio::DB::SeqFeature::Store::DBI::Iterator.3 \
Bio::DB::SeqFeature::Store::DBI::mysql.3 \
+ Bio::DB::SeqFeature::Store::DBI::Pg.3 \
+ Bio::DB::SeqFeature::Store::DBI::SQLite.3 \
+ Bio::DB::SeqFeature::Store::berkeleydb3.3 \
Bio::DB::SeqFeature::Store::FeatureFileLoader.3 \
Bio::DB::SeqFeature::Store::GFF2Loader.3 \
Bio::DB::SeqFeature::Store::GFF3Loader.3 \
@@ -650,6 +654,9 @@ MAN3= Bio::Align::AlignI.3 \
Bio::Search::Result::WABAResult.3 \
Bio::Search::SearchUtils.3 \
Bio::Search::StatisticsI.3 \
+ Bio::Search::Tiling::MapTileUtils.3 \
+ Bio::Search::Tiling::MapTiling.3 \
+ Bio::Search::Tiling::TilingI.3 \
Bio::SearchDist.3 \
Bio::SearchIO.3 \
Bio::SearchIO::EventHandlerI.3 \
@@ -678,6 +685,7 @@ MAN3= Bio::Align::AlignI.3 \
Bio::SearchIO::hmmer.3 \
Bio::SearchIO::hmmer_pull.3 \
Bio::SearchIO::infernal.3 \
+ Bio::SearchIO::gmap_f9.3 \
Bio::SearchIO::megablast.3 \
Bio::SearchIO::psl.3 \
Bio::SearchIO::rnamotif.3 \
@@ -861,6 +869,7 @@ MAN3= Bio::Align::AlignI.3 \
Bio::Tools::EUtilities::Summary.3 \
Bio::Tools::EUtilities::Summary::DocSum.3 \
Bio::Tools::EUtilities::Summary::Item.3 \
+ Bio::Tools::EUtilities::Summary::ItemContainerI.3 \
Bio::Tools::Eponine.3 \
Bio::Tools::Est2Genome.3 \
Bio::Tools::Fgenesh.3 \
@@ -875,7 +884,6 @@ MAN3= Bio::Align::AlignI.3 \
Bio::Tools::Glimmer.3 \
Bio::Tools::Grail.3 \
Bio::Tools::GuessSeqFormat.3 \
- Bio::Tools::HMM.3 \
Bio::Tools::HMMER::Domain.3 \
Bio::Tools::HMMER::Results.3 \
Bio::Tools::HMMER::Set.3 \
@@ -919,6 +927,7 @@ MAN3= Bio::Align::AlignI.3 \
Bio::Tools::Run::StandAloneWUBlast.3 \
Bio::Tools::Run::WrapperBase.3 \
Bio::Tools::Seg.3 \
+ Bio::Tools::SeqPattern::Backtranslate.3 \
Bio::Tools::SeqPattern.3 \
Bio::Tools::SeqStats.3 \
Bio::Tools::SeqWords.3 \
@@ -987,7 +996,7 @@ post-install:
${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR}
.if !defined(NOPORTDOCS)
${MKDIR} ${DOCSDIR}
-.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST PLATFORMS README
+.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST README
${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR}
.endfor
${CP} -R ${WRKSRC}/doc ${DOCSDIR}
diff --git a/biology/p5-bioperl/distinfo b/biology/p5-bioperl/distinfo
index 2908ee9e9b2..741f693e651 100644
--- a/biology/p5-bioperl/distinfo
+++ b/biology/p5-bioperl/distinfo
@@ -1,3 +1,3 @@
-MD5 (BioPerl-1.6.0.tar.gz) = ce38cba5f06aaf3c692c1a32218cde87
-SHA256 (BioPerl-1.6.0.tar.gz) = 46d7fce2a20128f8515a9690feb27d9fd65023a2f85c83dca781d0aa1ba1e889
-SIZE (BioPerl-1.6.0.tar.gz) = 6813396
+MD5 (BioPerl-1.6.1.tar.gz) = aa88f122c10714fd27beea4b70b659ad
+SHA256 (BioPerl-1.6.1.tar.gz) = ac36dace2b4dd973567b02cce29158beac05fd672872ca8769e02bbddddc95a3
+SIZE (BioPerl-1.6.1.tar.gz) = 10462526
diff --git a/biology/p5-bioperl/files/patch-Build.pm b/biology/p5-bioperl/files/patch-Bio-Root-Build.pm
index bdca7e89404..0b1369eb05e 100644
--- a/biology/p5-bioperl/files/patch-Build.pm
+++ b/biology/p5-bioperl/files/patch-Bio-Root-Build.pm
@@ -1,10 +1,10 @@
---- Bio/Root/Build.pm.orig 2009-01-25 02:19:26.000000000 -0300
-+++ Bio/Root/Build.pm 2009-02-22 02:24:05.000000000 -0300
-@@ -141,48 +141,8 @@
+--- Bio/Root/Build.pm.orig 2009-09-30 00:33:53.000000000 +0800
++++ Bio/Root/Build.pm 2009-12-01 10:31:39.000000000 +0800
+@@ -124,48 +124,8 @@
}
}
closedir($scripts_dir);
-- my $question = $int_ok ? "Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively?" : "Install [a]ll Bioperl scripts or [n]one?";
+- my $question = $int_ok ? "Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively?" : "Install [a]ll BioPerl scripts or [n]one?";
-
- my $prompt = $accept ? 'a' : $self->prompt($question, 'a');
-
@@ -47,11 +47,11 @@
- }
-
+ $self->log_info(" - will install all scripts\n");
-+ $self->notes(chosen_scripts => 'all');
++ $self->notes(chosen_scripts => 'all');
print "\n";
}
-@@ -1177,16 +1137,9 @@
+@@ -1205,16 +1165,9 @@
sub prompt_for_network {
my ($self, $accept) = @_;
diff --git a/biology/p5-bioperl/files/patch-Build.PL b/biology/p5-bioperl/files/patch-Build.PL
index b6f498ff750..5e617cc16be 100644
--- a/biology/p5-bioperl/files/patch-Build.PL
+++ b/biology/p5-bioperl/files/patch-Build.PL
@@ -1,6 +1,6 @@
---- Build.PL.orig 2009-01-25 02:19:13.000000000 -0300
-+++ Build.PL 2009-02-22 02:21:33.000000000 -0300
-@@ -36,7 +36,7 @@
+--- Build.PL.orig 2009-09-30 00:33:45.000000000 +0800
++++ Build.PL 2009-12-01 10:25:51.000000000 +0800
+@@ -37,7 +37,7 @@
'Test::More' => 0,
'Module::Build' => 0.2805,
'Test::Harness' => 2.62,
@@ -9,7 +9,7 @@
},
recommends => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
'Ace' => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
-@@ -214,83 +214,8 @@
+@@ -234,86 +234,9 @@
sub prompt_for_biodb {
my $accept = shift;
@@ -19,7 +19,7 @@
-
- if ($proceed) {
- my @driver_choices;
-- foreach my $poss ('mysql', 'Pg', 'Oracle') {
+- foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') {
- if (grep {/$poss/i} @drivers) {
- my $choice = $poss;
- $choice =~ s/^(.)/[$1]/;
@@ -44,6 +44,9 @@
- elsif ($driver =~ /^[oO]/) {
- $driver = 'Oracle';
- }
+- elsif ($driver =~ /^[sS]/) {
+- $driver = 'SQLite';
+- }
-
- my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n".
- "This database should already be present but doesn't have to ".
@@ -58,7 +61,7 @@
- }
-
- my $test_dsn;
-- if ($driver eq 'Pg') {
+- if ($driver eq 'Pg' || $driver eq 'SQLite') {
- $test_dsn = "dbi:$driver:dbname=$test_db";
- $mysql_ok = 0;
- }
@@ -84,12 +87,12 @@
- " User $test_user\n",
- " Password $test_pass\n");
- $build->log_info(" - will not run the BioDBSeqFeature live ".
-- "database tests (requires MySQL driver)\n") unless ($driver eq 'mysql');
+- "database tests (requires MySQL or Pg driver)\n") unless ($driver eq 'mysql' or $driver eq 'Pg');
- }
- else {
- $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
- }
--
+
+ my $proceed = 0;
+ $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
$build->log_info("\n");
diff --git a/biology/p5-bioperl/pkg-plist b/biology/p5-bioperl/pkg-plist
index b9fb7f56c3f..f330a94e767 100644
--- a/biology/p5-bioperl/pkg-plist
+++ b/biology/p5-bioperl/pkg-plist
@@ -1,1099 +1,1155 @@
-bin/bp_sreformat.pl
-bin/bp_seqconvert.pl
-bin/bp_parse_hmmsearch.pl
-bin/bp_seqret.pl
-bin/bp_tree2pag.pl
-bin/bp_meta_gff.pl
-bin/bp_nexus2nh.pl
-bin/bp_filter_search.pl
-bin/bp_flanks.pl
-bin/bp_seqfeature_gff3.pl
-bin/bp_generate_histogram.pl
-bin/bp_heterogeneity_test.pl
-bin/bp_split_seq.pl
-bin/bp_load_gff.pl
-bin/bp_biogetseq.pl
-bin/bp_fetch.pl
-bin/bp_mutate.pl
-bin/bp_process_sgd.pl
-bin/bp_index.pl
-bin/bp_dbsplit.pl
-bin/bp_oligo_count.pl
-bin/bp_seq_length.pl
-bin/bp_seqfeature_load.pl
-bin/bp_process_gadfly.pl
-bin/bp_hmmer_to_table.pl
-bin/bp_fastam9_to_table.pl
-bin/bp_genbank2gff.pl
-bin/bp_biofetch_genbank_proxy.pl
-bin/bp_extract_feature_seq.pl
-bin/bp_search2gff.pl
-bin/bp_taxid4species.pl
-bin/bp_bulk_load_gff.pl
-bin/bp_blast2tree.pl
-bin/bp_make_mrna_protein.pl
-bin/bp_unflatten_seq.pl
-bin/bp_search2tribe.pl
-bin/bp_bioflat_index.pl
-bin/bp_seqfeature_delete.pl
-bin/bp_query_entrez_taxa.pl
-bin/bp_pairwise_kaks.pl
-bin/bp_fast_load_gff.pl
-bin/bp_chaos_plot.pl
-bin/bp_taxonomy2tree.pl
-bin/bp_mrtrans.pl
-bin/bp_search2alnblocks.pl
-bin/bp_download_query_genbank.pl
-bin/bp_nrdb.pl
-bin/bp_mask_by_search.pl
-bin/bp_gccalc.pl
-bin/bp_composite_LD.pl
-bin/bp_classify_hits_kingdom.pl
-bin/bp_aacomp.pl
-bin/bp_process_wormbase.pl
-bin/bp_local_taxonomydb_query.pl
-bin/bp_biblio.pl
-bin/bp_seqretsplit.pl
-bin/bp_remote_blast.pl
-bin/bp_genbank2gff3.pl
-bin/bp_search2table.pl
-bin/bp_search2BSML.pl
-bin/bp_translate_seq.pl
-bin/bp_pg_bulk_load_gff.pl
-%%SITE_PERL%%/Bio/Align/Utilities.pm
+%%DATADIR%%/models/README
+%%DATADIR%%/models/biblio.dia
+%%DATADIR%%/models/bio_liveseq_variation.dia
+%%DATADIR%%/models/bio_map.dia
+%%DATADIR%%/models/bioperl.dia
+%%DATADIR%%/models/bio_restriction.dia
+%%DATADIR%%/models/coordinatemapper.dia
+%%DATADIR%%/models/map_proposal.txt
+%%DATADIR%%/models/maps_and_markers.dia
+%%DATADIR%%/models/popgen.dia
+%%DATADIR%%/models/population_proposal.txt
+%%DATADIR%%/scripts/Bio-DB-EUtilities/einfo.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/README
+%%DATADIR%%/scripts/Bio-DB-GFF/bulk_load_gff.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/fast_load_gff.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/genbank2gff3.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/genbank2gff.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/generate_histogram.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/load_gff.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/meta_gff.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/process_gadfly.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/process_sgd.PLS
+%%DATADIR%%/scripts/Bio-DB-GFF/process_wormbase.PLS
+%%DATADIR%%/scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
+%%DATADIR%%/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
+%%DATADIR%%/scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
+%%DATADIR%%/scripts/DB-HIV/hivq.PLS
+%%DATADIR%%/scripts/DB/TAG
+%%DATADIR%%/scripts/DB/biofetch_genbank_proxy.PLS
+%%DATADIR%%/scripts/DB/bioflat_index.PLS
+%%DATADIR%%/scripts/DB/biogetseq.PLS
+%%DATADIR%%/scripts/DB/flanks.PLS
+%%DATADIR%%/scripts/README
+%%DATADIR%%/scripts/biblio/TAG
+%%DATADIR%%/scripts/biblio/biblio.PLS
+%%DATADIR%%/scripts/das/README
+%%DATADIR%%/scripts/das/TAG
+%%DATADIR%%/scripts/index/TAG
+%%DATADIR%%/scripts/index/bp_fetch.PLS
+%%DATADIR%%/scripts/index/bp_index.PLS
+%%DATADIR%%/scripts/index/bp_seqret.PLS
+%%DATADIR%%/scripts/popgen/composite_LD.PLS
+%%DATADIR%%/scripts/popgen/heterogeneity_test.PLS
+%%DATADIR%%/scripts/searchio/README
+%%DATADIR%%/scripts/searchio/TAG
+%%DATADIR%%/scripts/searchio/fastam9_to_table.PLS
+%%DATADIR%%/scripts/searchio/filter_search.PLS
+%%DATADIR%%/scripts/searchio/hmmer_to_table.PLS
+%%DATADIR%%/scripts/searchio/parse_hmmsearch.PLS
+%%DATADIR%%/scripts/searchio/search2table.PLS
+%%DATADIR%%/scripts/seq/TAG
+%%DATADIR%%/scripts/seq/extract_feature_seq.PLS
+%%DATADIR%%/scripts/seq/make_mrna_protein.PLS
+%%DATADIR%%/scripts/seq/seqconvert.PLS
+%%DATADIR%%/scripts/seq/seqretsplit.PLS
+%%DATADIR%%/scripts/seq/split_seq.PLS
+%%DATADIR%%/scripts/seqstats/TAG
+%%DATADIR%%/scripts/seqstats/aacomp.PLS
+%%DATADIR%%/scripts/seqstats/chaos_plot.PLS
+%%DATADIR%%/scripts/seqstats/gccalc.PLS
+%%DATADIR%%/scripts/seqstats/oligo_count.PLS
+%%DATADIR%%/scripts/seq/translate_seq.PLS
+%%DATADIR%%/scripts/seq/unflatten_seq.PLS
+%%DATADIR%%/scripts/taxa/TAG
+%%DATADIR%%/scripts/taxa/classify_hits_kingdom.PLS
+%%DATADIR%%/scripts/taxa/local_taxonomydb_query.PLS
+%%DATADIR%%/scripts/taxa/query_entrez_taxa.PLS
+%%DATADIR%%/scripts/taxa/taxid4species.PLS
+%%DATADIR%%/scripts/taxa/taxonomy2tree.PLS
+%%DATADIR%%/scripts/tree/TAG
+%%DATADIR%%/scripts/tree/blast2tree.PLS
+%%DATADIR%%/scripts/tree/nexus2nh.PLS
+%%DATADIR%%/scripts/tree/tree2pag.PLS
+%%DATADIR%%/scripts/utilities/README
+%%DATADIR%%/scripts/utilities/TAG
+%%DATADIR%%/scripts/utilities/bp_mrtrans.PLS
+%%DATADIR%%/scripts/utilities/bp_nrdb.PLS
+%%DATADIR%%/scripts/utilities/bp_sreformat.PLS
+%%DATADIR%%/scripts/utilities/dbsplit.PLS
+%%DATADIR%%/scripts/utilities/download_query_genbank.PLS
+%%DATADIR%%/scripts/utilities/mask_by_search.PLS
+%%DATADIR%%/scripts/utilities/mutate.PLS
+%%DATADIR%%/scripts/utilities/pairwise_kaks.PLS
+%%DATADIR%%/scripts/utilities/remote_blast.PLS
+%%DATADIR%%/scripts/utilities/revtrans-motif.PLS
+%%DATADIR%%/scripts/utilities/search2BSML.PLS
+%%DATADIR%%/scripts/utilities/search2alnblocks.PLS
+%%DATADIR%%/scripts/utilities/search2gff.PLS
+%%DATADIR%%/scripts/utilities/search2tribe.PLS
+%%DATADIR%%/scripts/utilities/seq_length.PLS
+%%EXAMPLESDIR%%/Bio-DB-GFF/load_ucsc.pl
+%%EXAMPLESDIR%%/align/align_on_codons.pl
+%%EXAMPLESDIR%%/align/aligntutorial.pl
+%%EXAMPLESDIR%%/align/clustalw.pl
+%%EXAMPLESDIR%%/align/simplealign.pl
+%%EXAMPLESDIR%%/biblio/biblio-eutils-example.pl
+%%EXAMPLESDIR%%/biblio/biblio-soap-example.pl
+%%EXAMPLESDIR%%/biblio/biblio_soap.pl
+%%EXAMPLESDIR%%/bioperl.pl
+%%EXAMPLESDIR%%/cluster/dbsnp.pl
+%%EXAMPLESDIR%%/contributed/nmrpdb_parse.pl
+%%EXAMPLESDIR%%/contributed/prosite2perl.pl
+%%EXAMPLESDIR%%/contributed/rebase2list.pl
+%%EXAMPLESDIR%%/db/dbfetch
+%%EXAMPLESDIR%%/db/est_tissue_query.pl
+%%EXAMPLESDIR%%/db/gb2features.pl
+%%EXAMPLESDIR%%/db/getGenBank.pl
+%%EXAMPLESDIR%%/db/get_seqs.pl
+%%EXAMPLESDIR%%/db/rfetch.pl
+%%EXAMPLESDIR%%/db/use_registry.pl
+%%EXAMPLESDIR%%/generate_random_seq.pl
+%%EXAMPLESDIR%%/liveseq/change_gene.pl
+%%EXAMPLESDIR%%/longorf.pl
+%%EXAMPLESDIR%%/make_primers.pl
+%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl
+%%EXAMPLESDIR%%/quality/svgtrace.pl
+%%EXAMPLESDIR%%/rev_and_trans.pl
+%%EXAMPLESDIR%%/revcom_dir.pl
+%%EXAMPLESDIR%%/root/README
+%%EXAMPLESDIR%%/root/exceptions1.pl
+%%EXAMPLESDIR%%/root/exceptions2.pl
+%%EXAMPLESDIR%%/root/exceptions3.pl
+%%EXAMPLESDIR%%/root/exceptions4.pl
+%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeqI.pm
+%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeq.pm
+%%EXAMPLESDIR%%/root/lib/Bio/SeqI.pm
+%%EXAMPLESDIR%%/root/lib/Bio/Seq.pm
+%%EXAMPLESDIR%%/root/lib/TestInterface.pm
+%%EXAMPLESDIR%%/root/lib/TestObject.pm
+%%EXAMPLESDIR%%/searchio/blast_example.pl
+%%EXAMPLESDIR%%/searchio/custom_writer.pl
+%%EXAMPLESDIR%%/searchio/hitwriter.pl
+%%EXAMPLESDIR%%/searchio/hspwriter.pl
+%%EXAMPLESDIR%%/searchio/htmlwriter.pl
+%%EXAMPLESDIR%%/searchio/psiblast_features.pl
+%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl
+%%EXAMPLESDIR%%/searchio/rawwriter.pl
+%%EXAMPLESDIR%%/searchio/resultwriter.pl
+%%EXAMPLESDIR%%/searchio/waba2gff3.pl
+%%EXAMPLESDIR%%/searchio/waba2gff.pl
+%%EXAMPLESDIR%%/sirna/TAG
+%%EXAMPLESDIR%%/sirna/rnai_finder.cgi
+%%EXAMPLESDIR%%/structure/structure-io.pl
+%%EXAMPLESDIR%%/subsequence.cgi
+%%EXAMPLESDIR%%/tk/gsequence.pl
+%%EXAMPLESDIR%%/tk/hitdisplay.pl
+%%EXAMPLESDIR%%/tools/extract_genes.pl
+%%EXAMPLESDIR%%/tools/gb_to_gff.pl
+%%EXAMPLESDIR%%/tools/gff2ps.pl
+%%EXAMPLESDIR%%/tools/parse_codeml.pl
+%%EXAMPLESDIR%%/tools/psw.pl
+%%EXAMPLESDIR%%/tools/reverse-translate.pl
+%%EXAMPLESDIR%%/tools/run_genscan.pl
+%%EXAMPLESDIR%%/tools/run_primer3.pl
+%%EXAMPLESDIR%%/tools/seq_pattern.pl
+%%EXAMPLESDIR%%/tools/standaloneblast.pl
+%%EXAMPLESDIR%%/tree/paup2phylip.pl
+%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
+%%PORTDOCS%%%%DOCSDIR%%/BUGS
+%%PORTDOCS%%%%DOCSDIR%%/Changes
+%%PORTDOCS%%%%DOCSDIR%%/DEPENDENCIES
+%%PORTDOCS%%%%DOCSDIR%%/DEPRECATED
+%%PORTDOCS%%%%DOCSDIR%%/INSTALL
+%%PORTDOCS%%%%DOCSDIR%%/LICENSE
+%%PORTDOCS%%%%DOCSDIR%%/MANIFEST
+%%PORTDOCS%%%%DOCSDIR%%/README
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-%%DATADIR%%/models/README
-%%DATADIR%%/models/bio_liveseq_variation.dia
-%%DATADIR%%/models/bio_map.dia
-%%DATADIR%%/models/bio_restriction.dia
-%%DATADIR%%/models/bioperl.dia
-%%DATADIR%%/models/coordinatemapper.dia
-%%DATADIR%%/models/map_proposal.txt
-%%DATADIR%%/models/maps_and_markers.dia
-%%DATADIR%%/models/popgen.dia
-%%DATADIR%%/models/population_proposal.txt
-%%DATADIR%%/models/biblio.dia
-%%DATADIR%%/scripts/popgen/composite_LD.PLS
-%%DATADIR%%/scripts/popgen/heterogeneity_test.PLS
-%%DATADIR%%/scripts/Bio-DB-GFF/README
-%%DATADIR%%/scripts/Bio-DB-GFF/fast_load_gff.PLS
-%%DATADIR%%/scripts/Bio-DB-GFF/genbank2gff.PLS
-%%DATADIR%%/scripts/Bio-DB-GFF/genbank2gff3.PLS
-%%DATADIR%%/scripts/Bio-DB-GFF/generate_histogram.PLS
-%%DATADIR%%/scripts/Bio-DB-GFF/load_gff.PLS
-%%DATADIR%%/scripts/Bio-DB-GFF/meta_gff.PLS
-%%DATADIR%%/scripts/Bio-DB-GFF/process_gadfly.PLS
-%%DATADIR%%/scripts/Bio-DB-GFF/process_sgd.PLS
-%%DATADIR%%/scripts/Bio-DB-GFF/process_wormbase.PLS
-%%DATADIR%%/scripts/Bio-DB-GFF/bulk_load_gff.PLS
-%%DATADIR%%/scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
-%%DATADIR%%/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
-%%DATADIR%%/scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
-%%DATADIR%%/scripts/das/README
-%%DATADIR%%/scripts/das/TAG
-%%DATADIR%%/scripts/DB/biofetch_genbank_proxy.PLS
-%%DATADIR%%/scripts/DB/bioflat_index.PLS
-%%DATADIR%%/scripts/DB/biogetseq.PLS
-%%DATADIR%%/scripts/DB/flanks.PLS
-%%DATADIR%%/scripts/DB/TAG
-%%DATADIR%%/scripts/index/bp_fetch.PLS
-%%DATADIR%%/scripts/index/bp_index.PLS
-%%DATADIR%%/scripts/index/bp_seqret.PLS
-%%DATADIR%%/scripts/index/TAG
-%%DATADIR%%/scripts/tree/blast2tree.PLS
-%%DATADIR%%/scripts/tree/nexus2nh.PLS
-%%DATADIR%%/scripts/tree/TAG
-%%DATADIR%%/scripts/tree/tree2pag.PLS
-%%DATADIR%%/scripts/biblio/biblio.PLS
-%%DATADIR%%/scripts/biblio/TAG
-%%DATADIR%%/scripts/searchio/parse_hmmsearch.PLS
-%%DATADIR%%/scripts/searchio/filter_search.PLS
-%%DATADIR%%/scripts/searchio/hmmer_to_table.PLS
-%%DATADIR%%/scripts/searchio/fastam9_to_table.PLS
-%%DATADIR%%/scripts/searchio/README
-%%DATADIR%%/scripts/searchio/search2table.PLS
-%%DATADIR%%/scripts/searchio/TAG
-%%DATADIR%%/scripts/seq/unflatten_seq.PLS
-%%DATADIR%%/scripts/seq/make_mrna_protein.PLS
-%%DATADIR%%/scripts/seq/seqconvert.PLS
-%%DATADIR%%/scripts/seq/seqretsplit.PLS
-%%DATADIR%%/scripts/seq/split_seq.PLS
-%%DATADIR%%/scripts/seq/TAG
-%%DATADIR%%/scripts/seq/translate_seq.PLS
-%%DATADIR%%/scripts/seq/extract_feature_seq.PLS
-%%DATADIR%%/scripts/seqstats/aacomp.PLS
-%%DATADIR%%/scripts/seqstats/chaos_plot.PLS
-%%DATADIR%%/scripts/seqstats/gccalc.PLS
-%%DATADIR%%/scripts/seqstats/oligo_count.PLS
-%%DATADIR%%/scripts/seqstats/TAG
-%%DATADIR%%/scripts/taxa/classify_hits_kingdom.PLS
-%%DATADIR%%/scripts/taxa/local_taxonomydb_query.PLS
-%%DATADIR%%/scripts/taxa/query_entrez_taxa.PLS
-%%DATADIR%%/scripts/taxa/TAG
-%%DATADIR%%/scripts/taxa/taxid4species.PLS
-%%DATADIR%%/scripts/taxa/taxonomy2tree.PLS
-%%DATADIR%%/scripts/utilities/TAG
-%%DATADIR%%/scripts/utilities/bp_nrdb.PLS
-%%DATADIR%%/scripts/utilities/bp_sreformat.PLS
-%%DATADIR%%/scripts/utilities/dbsplit.PLS
-%%DATADIR%%/scripts/utilities/download_query_genbank.PLS
-%%DATADIR%%/scripts/utilities/mask_by_search.PLS
-%%DATADIR%%/scripts/utilities/mutate.PLS
-%%DATADIR%%/scripts/utilities/pairwise_kaks.PLS
-%%DATADIR%%/scripts/utilities/README
-%%DATADIR%%/scripts/utilities/remote_blast.PLS
-%%DATADIR%%/scripts/utilities/search2alnblocks.PLS
-%%DATADIR%%/scripts/utilities/search2BSML.PLS
-%%DATADIR%%/scripts/utilities/search2gff.PLS
-%%DATADIR%%/scripts/utilities/search2tribe.PLS
-%%DATADIR%%/scripts/utilities/seq_length.PLS
-%%DATADIR%%/scripts/utilities/bp_mrtrans.PLS
-%%DATADIR%%/scripts/README
+bin/bp_aacomp.pl
+bin/bp_biblio.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_dbsplit.pl
+bin/bp_download_query_genbank.pl
+bin/bp_einfo.pl
+bin/bp_extract_feature_seq.pl
+bin/bp_fastam9_to_table.pl
+bin/bp_fast_load_gff.pl
+bin/bp_fetch.pl
+bin/bp_filter_search.pl
+bin/bp_flanks.pl
+bin/bp_gccalc.pl
+bin/bp_genbank2gff3.pl
+bin/bp_genbank2gff.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_nexus2nh.pl
+bin/bp_nrdb.pl
+bin/bp_oligo_count.pl
+bin/bp_pairwise_kaks.pl
+bin/bp_parse_hmmsearch.pl
+bin/bp_pg_bulk_load_gff.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_seqconvert.pl
+bin/bp_seqfeature_delete.pl
+bin/bp_seqfeature_gff3.pl
+bin/bp_seqfeature_load.pl
+bin/bp_seq_length.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
+@dirrm %%DATADIR%%/scripts/Bio-DB-EUtilities
+@dirrm %%DATADIR%%/scripts/Bio-DB-GFF
+@dirrm %%DATADIR%%/scripts/Bio-SeqFeature-Store
+@dirrm %%DATADIR%%/scripts/DB
+@dirrm %%DATADIR%%/scripts/DB-HIV
+@dirrm %%DATADIR%%/scripts/biblio
+@dirrm %%DATADIR%%/scripts/das
+@dirrm %%DATADIR%%/scripts/index
+@dirrm %%DATADIR%%/scripts/popgen
+@dirrm %%DATADIR%%/scripts/searchio
+@dirrm %%DATADIR%%/scripts/seq
+@dirrm %%DATADIR%%/scripts/seqstats
+@dirrm %%DATADIR%%/scripts/taxa
+@dirrm %%DATADIR%%/scripts/tree
+@dirrm %%DATADIR%%/scripts/utilities
+@dirrm %%DATADIR%%/models
+@dirrm %%DATADIR%%/scripts
+@dirrm %%DATADIR%%
+@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
+@dirrm %%EXAMPLESDIR%%/align
+@dirrm %%EXAMPLESDIR%%/biblio
+@dirrm %%EXAMPLESDIR%%/cluster
+@dirrm %%EXAMPLESDIR%%/contributed
+@dirrm %%EXAMPLESDIR%%/db
+@dirrm %%EXAMPLESDIR%%/liveseq
+@dirrm %%EXAMPLESDIR%%/popgen
+@dirrm %%EXAMPLESDIR%%/quality
+@dirrm %%EXAMPLESDIR%%/root/lib/Bio
+@dirrm %%EXAMPLESDIR%%/root/lib
+@dirrm %%EXAMPLESDIR%%/root
+@dirrm %%EXAMPLESDIR%%/searchio
+@dirrm %%EXAMPLESDIR%%/sirna
+@dirrm %%EXAMPLESDIR%%/structure
+@dirrm %%EXAMPLESDIR%%/tk
+@dirrm %%EXAMPLESDIR%%/tools
+@dirrm %%EXAMPLESDIR%%/tree
+@dirrm %%EXAMPLESDIR%%
@dirrm %%SITE_PERL%%/Bio/Align
@dirrm %%SITE_PERL%%/Bio/AlignIO/Handler
@dirrm %%SITE_PERL%%/Bio/AlignIO
@@ -1146,10 +1202,10 @@ bin/bp_pg_bulk_load_gff.pl
@dirrm %%SITE_PERL%%/Bio/Matrix/PSM
@dirrm %%SITE_PERL%%/Bio/Matrix
@dirrm %%SITE_PERL%%/Bio/MolEvol
-@dirrm %%SITE_PERL%%/Bio/Ontology/SimpleGOEngine
-@dirrm %%SITE_PERL%%/Bio/Ontology
@dirrm %%SITE_PERL%%/Bio/OntologyIO/Handlers
@dirrm %%SITE_PERL%%/Bio/OntologyIO
+@dirrm %%SITE_PERL%%/Bio/Ontology/SimpleGOEngine
+@dirrm %%SITE_PERL%%/Bio/Ontology
@dirrm %%SITE_PERL%%/Bio/Phenotype/MeSH
@dirrm %%SITE_PERL%%/Bio/Phenotype/OMIM
@dirrm %%SITE_PERL%%/Bio/Phenotype
@@ -1157,21 +1213,20 @@ bin/bp_pg_bulk_load_gff.pl
@dirrm %%SITE_PERL%%/Bio/PopGen/IO
@dirrm %%SITE_PERL%%/Bio/PopGen/Simulation
@dirrm %%SITE_PERL%%/Bio/PopGen
-@dirrm %%SITE_PERL%%/Bio/Root/Test
-@dirrm %%SITE_PERL%%/Bio/Root
@dirrm %%SITE_PERL%%/Bio/Restriction/Enzyme
@dirrm %%SITE_PERL%%/Bio/Restriction/IO
@dirrm %%SITE_PERL%%/Bio/Restriction
+@dirrm %%SITE_PERL%%/Bio/Root/Test
+@dirrm %%SITE_PERL%%/Bio/Root
@dirrm %%SITE_PERL%%/Bio/Search/HSP
@dirrm %%SITE_PERL%%/Bio/Search/Hit
-@dirrm %%SITE_PERL%%/Bio/Search/Iteration
-@dirrm %%SITE_PERL%%/Bio/Search/Result
-@dirrm %%SITE_PERL%%/Bio/Search
@dirrm %%SITE_PERL%%/Bio/SearchIO/Writer
@dirrm %%SITE_PERL%%/Bio/SearchIO/XML
@dirrm %%SITE_PERL%%/Bio/SearchIO
-@dirrm %%SITE_PERL%%/Bio/Seq/Meta
-@dirrm %%SITE_PERL%%/Bio/Seq
+@dirrm %%SITE_PERL%%/Bio/Search/Iteration
+@dirrm %%SITE_PERL%%/Bio/Search/Result
+@dirrm %%SITE_PERL%%/Bio/Search/Tiling
+@dirrm %%SITE_PERL%%/Bio/Search
@dirrm %%SITE_PERL%%/Bio/SeqEvolution
@dirrm %%SITE_PERL%%/Bio/SeqFeature/Gene
@dirrm %%SITE_PERL%%/Bio/SeqFeature/SiRNA
@@ -1181,6 +1236,8 @@ bin/bp_pg_bulk_load_gff.pl
@dirrm %%SITE_PERL%%/Bio/SeqIO/game
@dirrm %%SITE_PERL%%/Bio/SeqIO/tinyseq
@dirrm %%SITE_PERL%%/Bio/SeqIO
+@dirrm %%SITE_PERL%%/Bio/Seq/Meta
+@dirrm %%SITE_PERL%%/Bio/Seq
@dirrm %%SITE_PERL%%/Bio/Structure/IO
@dirrm %%SITE_PERL%%/Bio/Structure/SecStr/DSSP
@dirrm %%SITE_PERL%%/Bio/Structure/SecStr/STRIDE
@@ -1207,6 +1264,7 @@ bin/bp_pg_bulk_load_gff.pl
@dirrm %%SITE_PERL%%/Bio/Tools/Primer/Assessor
@dirrm %%SITE_PERL%%/Bio/Tools/Primer
@dirrm %%SITE_PERL%%/Bio/Tools/Run
+@dirrm %%SITE_PERL%%/Bio/Tools/SeqPattern
@dirrm %%SITE_PERL%%/Bio/Tools/SiRNA/Ruleset
@dirrm %%SITE_PERL%%/Bio/Tools/SiRNA
@dirrm %%SITE_PERL%%/Bio/Tools/Signalp
@@ -1218,46 +1276,3 @@ bin/bp_pg_bulk_load_gff.pl
@dirrm %%SITE_PERL%%/Bio/TreeIO
@dirrm %%SITE_PERL%%/Bio/Variation/IO
@dirrm %%SITE_PERL%%/Bio/Variation
-@dirrm %%SITE_PERL%%/Bio
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/lib
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/bin
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/cgi-bin
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/t
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrm %%EXAMPLESDIR%%/root/lib/Bio
-@dirrm %%EXAMPLESDIR%%/root/lib
-@dirrm %%EXAMPLESDIR%%/root
-@dirrm %%EXAMPLESDIR%%/tools
-@dirrm %%EXAMPLESDIR%%/tk
-@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF
-@dirrm %%EXAMPLESDIR%%/structure
-@dirrm %%EXAMPLESDIR%%/sirna
-@dirrm %%EXAMPLESDIR%%/searchio
-@dirrm %%EXAMPLESDIR%%/db
-@dirrm %%EXAMPLESDIR%%/align
-@dirrm %%EXAMPLESDIR%%/biblio
-@dirrm %%EXAMPLESDIR%%/quality
-@dirrm %%EXAMPLESDIR%%/tree
-@dirrm %%EXAMPLESDIR%%/cluster
-@dirrm %%EXAMPLESDIR%%/contributed
-@dirrm %%EXAMPLESDIR%%/liveseq
-@dirrm %%EXAMPLESDIR%%/popgen
-@dirrm %%EXAMPLESDIR%%
-@dirrm %%DATADIR%%/models
-@dirrm %%DATADIR%%/scripts/popgen
-@dirrm %%DATADIR%%/scripts/Bio-DB-GFF
-@dirrm %%DATADIR%%/scripts/Bio-SeqFeature-Store
-@dirrm %%DATADIR%%/scripts/das
-@dirrm %%DATADIR%%/scripts/DB
-@dirrm %%DATADIR%%/scripts/index
-@dirrm %%DATADIR%%/scripts/tree
-@dirrm %%DATADIR%%/scripts/biblio
-@dirrm %%DATADIR%%/scripts/searchio
-@dirrm %%DATADIR%%/scripts/seq
-@dirrm %%DATADIR%%/scripts/seqstats
-@dirrm %%DATADIR%%/scripts/taxa
-@dirrm %%DATADIR%%/scripts/utilities
-@dirrm %%DATADIR%%/scripts
-@dirrm %%DATADIR%%
generated by cgit (git 2.34.1) at 2024-12-19 11:32:55 +0800