maint: restructure to use Dist::Zilla
commite2ca344775f9067a954331db89d4c79eedaf0315
authorCarnë Draug <carandraug+dev@gmail.com>
Mon, 17 Sep 2018 16:00:28 +0000 (17 17:00 +0100)
committerCarnë Draug <carandraug+dev@gmail.com>
Mon, 17 Sep 2018 21:12:53 +0000 (17 22:12 +0100)
treef5517dfeb52a7607b628bc5ef739be565398d2d0
parent9293a9b16ef25cc1a9613009ecb3c406bc1473f4
maint: restructure to use Dist::Zilla

* dist.ini: add to configure dzil.  Makes use of our Dist Zilla
  BioPerl pluginbundle.

* Bio/Root/Test.pm: use Test::RequiresInternet instead of the
  Module::Build used previously.

* t/PodSyntax.t: remove since it's generated automatically during
  the build step.

* Bio/ => lib/Bio: move all modules into lib.

* scripts/*/ => bin/: move all scripts into bin.  Also flatten
  its structure because the scripts names must not clash.

* LICENSE: remove because it's added automatically dy dzil as part
  of the release.

* Build.PL, INSTALL.SKIP, MANIFEST.SKIP: removed, since they are
  no longer used.

* Bio/Root/Build.pm: used by Build.PL which is no longer used so
  has been removed.

* .gitignore: ignore the builds made by dzil

The travis configuration is now broken.  Someone else that understands
it will need to fix it.  "Fixing" it by pushing incremental commits
until it works is not my thing.
752 files changed:
.gitignore
Bio/Root/Build.pm [deleted file]
Build.PL [deleted file]
Changes
INSTALL.SKIP [deleted file]
LICENSE [deleted file]
MANIFEST.SKIP [deleted file]
bin/bp_aacomp [moved from scripts/seqstats/bp_aacomp.pl with 100% similarity]
bin/bp_biofetch_genbank_proxy [moved from scripts/DB/bp_biofetch_genbank_proxy.pl with 100% similarity]
bin/bp_bioflat_index [moved from scripts/DB/bp_bioflat_index.pl with 100% similarity]
bin/bp_biogetseq [moved from scripts/DB/bp_biogetseq.pl with 100% similarity]
bin/bp_bulk_load_gff [moved from scripts/Bio-DB-GFF/bp_bulk_load_gff.pl with 100% similarity]
bin/bp_chaos_plot [moved from scripts/seqstats/bp_chaos_plot.pl with 100% similarity]
bin/bp_classify_hits_kingdom [moved from scripts/taxa/bp_classify_hits_kingdom.pl with 100% similarity]
bin/bp_das_server [moved from scripts/das/bp_das_server.pl with 100% similarity]
bin/bp_dbsplit [moved from scripts/utilities/bp_dbsplit.pl with 100% similarity]
bin/bp_download_query_genbank [moved from scripts/utilities/bp_download_query_genbank.pl with 100% similarity]
bin/bp_extract_feature_seq [moved from scripts/seq/bp_extract_feature_seq.pl with 100% similarity]
bin/bp_fast_load_gff [moved from scripts/Bio-DB-GFF/bp_fast_load_gff.pl with 100% similarity]
bin/bp_fastam9_to_table [moved from scripts/searchio/bp_fastam9_to_table.pl with 100% similarity]
bin/bp_fetch [moved from scripts/index/bp_fetch.pl with 100% similarity]
bin/bp_filter_search [moved from scripts/searchio/bp_filter_search.pl with 100% similarity]
bin/bp_find-blast-matches [moved from scripts/utilities/bp_find-blast-matches.pl with 100% similarity]
bin/bp_flanks [moved from scripts/DB/bp_flanks.pl with 100% similarity]
bin/bp_gccalc [moved from scripts/seqstats/bp_gccalc.pl with 100% similarity]
bin/bp_genbank2gff [moved from scripts/Bio-DB-GFF/bp_genbank2gff.pl with 100% similarity]
bin/bp_genbank2gff3 [moved from scripts/Bio-DB-GFF/bp_genbank2gff3.pl with 100% similarity]
bin/bp_generate_histogram [moved from scripts/Bio-DB-GFF/bp_generate_histogram.pl with 100% similarity]
bin/bp_index [moved from scripts/index/bp_index.pl with 100% similarity]
bin/bp_load_gff [moved from scripts/Bio-DB-GFF/bp_load_gff.pl with 100% similarity]
bin/bp_local_taxonomydb_query [moved from scripts/taxa/bp_local_taxonomydb_query.pl with 100% similarity]
bin/bp_make_mrna_protein [moved from scripts/seq/bp_make_mrna_protein.pl with 100% similarity]
bin/bp_mask_by_search [moved from scripts/utilities/bp_mask_by_search.pl with 100% similarity]
bin/bp_meta_gff [moved from scripts/Bio-DB-GFF/bp_meta_gff.pl with 100% similarity]
bin/bp_mrtrans [moved from scripts/utilities/bp_mrtrans.pl with 100% similarity]
bin/bp_mutate [moved from scripts/utilities/bp_mutate.pl with 100% similarity]
bin/bp_nexus2nh [moved from scripts/tree/bp_nexus2nh.pl with 100% similarity]
bin/bp_nrdb [moved from scripts/utilities/bp_nrdb.pl with 100% similarity]
bin/bp_oligo_count [moved from scripts/seqstats/bp_oligo_count.pl with 100% similarity]
bin/bp_process_gadfly [moved from scripts/Bio-DB-GFF/bp_process_gadfly.pl with 100% similarity]
bin/bp_process_sgd [moved from scripts/Bio-DB-GFF/bp_process_sgd.pl with 100% similarity]
bin/bp_query_entrez_taxa [moved from scripts/taxa/bp_query_entrez_taxa.pl with 100% similarity]
bin/bp_revtrans-motif [moved from scripts/utilities/bp_revtrans-motif.pl with 100% similarity]
bin/bp_search2alnblocks [moved from scripts/utilities/bp_search2alnblocks.pl with 100% similarity]
bin/bp_search2gff [moved from scripts/utilities/bp_search2gff.pl with 100% similarity]
bin/bp_search2table [moved from scripts/searchio/bp_search2table.pl with 100% similarity]
bin/bp_search2tribe [moved from scripts/utilities/bp_search2tribe.pl with 100% similarity]
bin/bp_seq_length [moved from scripts/utilities/bp_seq_length.pl with 100% similarity]
bin/bp_seqconvert [moved from scripts/seq/bp_seqconvert.pl with 100% similarity]
bin/bp_seqcut [moved from scripts/seq/bp_seqcut.pl with 100% similarity]
bin/bp_seqfeature_delete [moved from scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl with 100% similarity]
bin/bp_seqfeature_gff3 [moved from scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl with 100% similarity]
bin/bp_seqfeature_load [moved from scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl with 100% similarity]
bin/bp_seqpart [moved from scripts/seq/bp_seqpart.pl with 100% similarity]
bin/bp_seqret [moved from scripts/index/bp_seqret.pl with 100% similarity]
bin/bp_seqretsplit [moved from scripts/seq/bp_seqretsplit.pl with 100% similarity]
bin/bp_split_seq [moved from scripts/seq/bp_split_seq.pl with 100% similarity]
bin/bp_sreformat [moved from scripts/utilities/bp_sreformat.pl with 100% similarity]
bin/bp_taxid4species [moved from scripts/taxa/bp_taxid4species.pl with 100% similarity]
bin/bp_taxonomy2tree [moved from scripts/taxa/bp_taxonomy2tree.pl with 100% similarity]
bin/bp_translate_seq [moved from scripts/seq/bp_translate_seq.pl with 100% similarity]
bin/bp_tree2pag [moved from scripts/tree/bp_tree2pag.pl with 100% similarity]
bin/bp_unflatten_seq [moved from scripts/seq/bp_unflatten_seq.pl with 100% similarity]
dist.ini [new file with mode: 0644]
lib/Bio/Align/AlignI.pm [moved from Bio/Align/AlignI.pm with 100% similarity]
lib/Bio/Align/DNAStatistics.pm [moved from Bio/Align/DNAStatistics.pm with 100% similarity]
lib/Bio/Align/PairwiseStatistics.pm [moved from Bio/Align/PairwiseStatistics.pm with 100% similarity]
lib/Bio/Align/ProteinStatistics.pm [moved from Bio/Align/ProteinStatistics.pm with 100% similarity]
lib/Bio/Align/StatisticsI.pm [moved from Bio/Align/StatisticsI.pm with 100% similarity]
lib/Bio/Align/Utilities.pm [moved from Bio/Align/Utilities.pm with 100% similarity]
lib/Bio/AlignIO.pm [moved from Bio/AlignIO.pm with 100% similarity]
lib/Bio/AlignIO/Handler/GenericAlignHandler.pm [moved from Bio/AlignIO/Handler/GenericAlignHandler.pm with 100% similarity]
lib/Bio/AlignIO/arp.pm [moved from Bio/AlignIO/arp.pm with 100% similarity]
lib/Bio/AlignIO/bl2seq.pm [moved from Bio/AlignIO/bl2seq.pm with 100% similarity]
lib/Bio/AlignIO/clustalw.pm [moved from Bio/AlignIO/clustalw.pm with 100% similarity]
lib/Bio/AlignIO/emboss.pm [moved from Bio/AlignIO/emboss.pm with 100% similarity]
lib/Bio/AlignIO/fasta.pm [moved from Bio/AlignIO/fasta.pm with 100% similarity]
lib/Bio/AlignIO/largemultifasta.pm [moved from Bio/AlignIO/largemultifasta.pm with 100% similarity]
lib/Bio/AlignIO/maf.pm [moved from Bio/AlignIO/maf.pm with 100% similarity]
lib/Bio/AlignIO/mase.pm [moved from Bio/AlignIO/mase.pm with 100% similarity]
lib/Bio/AlignIO/mega.pm [moved from Bio/AlignIO/mega.pm with 100% similarity]
lib/Bio/AlignIO/meme.pm [moved from Bio/AlignIO/meme.pm with 100% similarity]
lib/Bio/AlignIO/metafasta.pm [moved from Bio/AlignIO/metafasta.pm with 100% similarity]
lib/Bio/AlignIO/msf.pm [moved from Bio/AlignIO/msf.pm with 100% similarity]
lib/Bio/AlignIO/nexus.pm [moved from Bio/AlignIO/nexus.pm with 100% similarity]
lib/Bio/AlignIO/pfam.pm [moved from Bio/AlignIO/pfam.pm with 100% similarity]
lib/Bio/AlignIO/phylip.pm [moved from Bio/AlignIO/phylip.pm with 100% similarity]
lib/Bio/AlignIO/po.pm [moved from Bio/AlignIO/po.pm with 100% similarity]
lib/Bio/AlignIO/proda.pm [moved from Bio/AlignIO/proda.pm with 100% similarity]
lib/Bio/AlignIO/prodom.pm [moved from Bio/AlignIO/prodom.pm with 100% similarity]
lib/Bio/AlignIO/psi.pm [moved from Bio/AlignIO/psi.pm with 100% similarity]
lib/Bio/AlignIO/selex.pm [moved from Bio/AlignIO/selex.pm with 100% similarity]
lib/Bio/AlignIO/xmfa.pm [moved from Bio/AlignIO/xmfa.pm with 100% similarity]
lib/Bio/AnalysisI.pm [moved from Bio/AnalysisI.pm with 100% similarity]
lib/Bio/AnalysisParserI.pm [moved from Bio/AnalysisParserI.pm with 100% similarity]
lib/Bio/AnalysisResultI.pm [moved from Bio/AnalysisResultI.pm with 100% similarity]
lib/Bio/AnnotatableI.pm [moved from Bio/AnnotatableI.pm with 100% similarity]
lib/Bio/Annotation/AnnotationFactory.pm [moved from Bio/Annotation/AnnotationFactory.pm with 100% similarity]
lib/Bio/Annotation/Collection.pm [moved from Bio/Annotation/Collection.pm with 100% similarity]
lib/Bio/Annotation/Comment.pm [moved from Bio/Annotation/Comment.pm with 100% similarity]
lib/Bio/Annotation/DBLink.pm [moved from Bio/Annotation/DBLink.pm with 100% similarity]
lib/Bio/Annotation/OntologyTerm.pm [moved from Bio/Annotation/OntologyTerm.pm with 100% similarity]
lib/Bio/Annotation/Reference.pm [moved from Bio/Annotation/Reference.pm with 100% similarity]
lib/Bio/Annotation/Relation.pm [moved from Bio/Annotation/Relation.pm with 100% similarity]
lib/Bio/Annotation/SimpleValue.pm [moved from Bio/Annotation/SimpleValue.pm with 100% similarity]
lib/Bio/Annotation/StructuredValue.pm [moved from Bio/Annotation/StructuredValue.pm with 100% similarity]
lib/Bio/Annotation/TagTree.pm [moved from Bio/Annotation/TagTree.pm with 100% similarity]
lib/Bio/Annotation/Target.pm [moved from Bio/Annotation/Target.pm with 100% similarity]
lib/Bio/Annotation/Tree.pm [moved from Bio/Annotation/Tree.pm with 100% similarity]
lib/Bio/Annotation/TypeManager.pm [moved from Bio/Annotation/TypeManager.pm with 100% similarity]
lib/Bio/AnnotationCollectionI.pm [moved from Bio/AnnotationCollectionI.pm with 100% similarity]
lib/Bio/AnnotationI.pm [moved from Bio/AnnotationI.pm with 100% similarity]
lib/Bio/Cluster/ClusterFactory.pm [moved from Bio/Cluster/ClusterFactory.pm with 100% similarity]
lib/Bio/Cluster/FamilyI.pm [moved from Bio/Cluster/FamilyI.pm with 100% similarity]
lib/Bio/Cluster/SequenceFamily.pm [moved from Bio/Cluster/SequenceFamily.pm with 100% similarity]
lib/Bio/Cluster/UniGene.pm [moved from Bio/Cluster/UniGene.pm with 100% similarity]
lib/Bio/Cluster/UniGeneI.pm [moved from Bio/Cluster/UniGeneI.pm with 100% similarity]
lib/Bio/ClusterI.pm [moved from Bio/ClusterI.pm with 100% similarity]
lib/Bio/ClusterIO.pm [moved from Bio/ClusterIO.pm with 100% similarity]
lib/Bio/ClusterIO/dbsnp.pm [moved from Bio/ClusterIO/dbsnp.pm with 100% similarity]
lib/Bio/ClusterIO/unigene.pm [moved from Bio/ClusterIO/unigene.pm with 100% similarity]
lib/Bio/CodonUsage/IO.pm [moved from Bio/CodonUsage/IO.pm with 100% similarity]
lib/Bio/CodonUsage/Table.pm [moved from Bio/CodonUsage/Table.pm with 100% similarity]
lib/Bio/DB/BioFetch.pm [moved from Bio/DB/BioFetch.pm with 100% similarity]
lib/Bio/DB/CUTG.pm [moved from Bio/DB/CUTG.pm with 100% similarity]
lib/Bio/DB/DBFetch.pm [moved from Bio/DB/DBFetch.pm with 100% similarity]
lib/Bio/DB/EMBL.pm [moved from Bio/DB/EMBL.pm with 100% similarity]
lib/Bio/DB/EntrezGene.pm [moved from Bio/DB/EntrezGene.pm with 100% similarity]
lib/Bio/DB/Failover.pm [moved from Bio/DB/Failover.pm with 100% similarity]
lib/Bio/DB/Fasta.pm [moved from Bio/DB/Fasta.pm with 100% similarity]
lib/Bio/DB/FileCache.pm [moved from Bio/DB/FileCache.pm with 100% similarity]
lib/Bio/DB/Flat.pm [moved from Bio/DB/Flat.pm with 100% similarity]
lib/Bio/DB/Flat/BDB.pm [moved from Bio/DB/Flat/BDB.pm with 100% similarity]
lib/Bio/DB/Flat/BDB/embl.pm [moved from Bio/DB/Flat/BDB/embl.pm with 100% similarity]
lib/Bio/DB/Flat/BDB/fasta.pm [moved from Bio/DB/Flat/BDB/fasta.pm with 100% similarity]
lib/Bio/DB/Flat/BDB/genbank.pm [moved from Bio/DB/Flat/BDB/genbank.pm with 100% similarity]
lib/Bio/DB/Flat/BDB/swiss.pm [moved from Bio/DB/Flat/BDB/swiss.pm with 100% similarity]
lib/Bio/DB/Flat/BinarySearch.pm [moved from Bio/DB/Flat/BinarySearch.pm with 100% similarity]
lib/Bio/DB/GFF.pm [moved from Bio/DB/GFF.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/berkeleydb.pm [moved from Bio/DB/GFF/Adaptor/berkeleydb.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm [moved from Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/biofetch.pm [moved from Bio/DB/GFF/Adaptor/biofetch.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/biofetch_oracle.pm [moved from Bio/DB/GFF/Adaptor/biofetch_oracle.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/dbi.pm [moved from Bio/DB/GFF/Adaptor/dbi.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm [moved from Bio/DB/GFF/Adaptor/dbi/caching_handle.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/dbi/iterator.pm [moved from Bio/DB/GFF/Adaptor/dbi/iterator.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/dbi/mysql.pm [moved from Bio/DB/GFF/Adaptor/dbi/mysql.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm [moved from Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm [moved from Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/dbi/oracle.pm [moved from Bio/DB/GFF/Adaptor/dbi/oracle.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/dbi/pg.pm [moved from Bio/DB/GFF/Adaptor/dbi/pg.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/dbi/pg_fts.pm [moved from Bio/DB/GFF/Adaptor/dbi/pg_fts.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/memory.pm [moved from Bio/DB/GFF/Adaptor/memory.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/memory/feature_serializer.pm [moved from Bio/DB/GFF/Adaptor/memory/feature_serializer.pm with 100% similarity]
lib/Bio/DB/GFF/Adaptor/memory/iterator.pm [moved from Bio/DB/GFF/Adaptor/memory/iterator.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator.pm [moved from Bio/DB/GFF/Aggregator.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/alignment.pm [moved from Bio/DB/GFF/Aggregator/alignment.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/clone.pm [moved from Bio/DB/GFF/Aggregator/clone.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/coding.pm [moved from Bio/DB/GFF/Aggregator/coding.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/gene.pm [moved from Bio/DB/GFF/Aggregator/gene.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/match.pm [moved from Bio/DB/GFF/Aggregator/match.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/none.pm [moved from Bio/DB/GFF/Aggregator/none.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/orf.pm [moved from Bio/DB/GFF/Aggregator/orf.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/processed_transcript.pm [moved from Bio/DB/GFF/Aggregator/processed_transcript.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/so_transcript.pm [moved from Bio/DB/GFF/Aggregator/so_transcript.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/transcript.pm [moved from Bio/DB/GFF/Aggregator/transcript.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/ucsc_acembly.pm [moved from Bio/DB/GFF/Aggregator/ucsc_acembly.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm [moved from Bio/DB/GFF/Aggregator/ucsc_ensgene.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/ucsc_genscan.pm [moved from Bio/DB/GFF/Aggregator/ucsc_genscan.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/ucsc_refgene.pm [moved from Bio/DB/GFF/Aggregator/ucsc_refgene.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm [moved from Bio/DB/GFF/Aggregator/ucsc_sanger22.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm [moved from Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/ucsc_softberry.pm [moved from Bio/DB/GFF/Aggregator/ucsc_softberry.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm [moved from Bio/DB/GFF/Aggregator/ucsc_twinscan.pm with 100% similarity]
lib/Bio/DB/GFF/Aggregator/ucsc_unigene.pm [moved from Bio/DB/GFF/Aggregator/ucsc_unigene.pm with 100% similarity]
lib/Bio/DB/GFF/Featname.pm [moved from Bio/DB/GFF/Featname.pm with 100% similarity]
lib/Bio/DB/GFF/Feature.pm [moved from Bio/DB/GFF/Feature.pm with 100% similarity]
lib/Bio/DB/GFF/Homol.pm [moved from Bio/DB/GFF/Homol.pm with 100% similarity]
lib/Bio/DB/GFF/RelSegment.pm [moved from Bio/DB/GFF/RelSegment.pm with 100% similarity]
lib/Bio/DB/GFF/Segment.pm [moved from Bio/DB/GFF/Segment.pm with 100% similarity]
lib/Bio/DB/GFF/Typename.pm [moved from Bio/DB/GFF/Typename.pm with 100% similarity]
lib/Bio/DB/GFF/Util/Binning.pm [moved from Bio/DB/GFF/Util/Binning.pm with 100% similarity]
lib/Bio/DB/GFF/Util/Rearrange.pm [moved from Bio/DB/GFF/Util/Rearrange.pm with 100% similarity]
lib/Bio/DB/GenBank.pm [moved from Bio/DB/GenBank.pm with 100% similarity]
lib/Bio/DB/GenPept.pm [moved from Bio/DB/GenPept.pm with 100% similarity]
lib/Bio/DB/GenericWebAgent.pm [moved from Bio/DB/GenericWebAgent.pm with 100% similarity]
lib/Bio/DB/InMemoryCache.pm [moved from Bio/DB/InMemoryCache.pm with 100% similarity]
lib/Bio/DB/IndexedBase.pm [moved from Bio/DB/IndexedBase.pm with 100% similarity]
lib/Bio/DB/LocationI.pm [moved from Bio/DB/LocationI.pm with 100% similarity]
lib/Bio/DB/NCBIHelper.pm [moved from Bio/DB/NCBIHelper.pm with 100% similarity]
lib/Bio/DB/Qual.pm [moved from Bio/DB/Qual.pm with 100% similarity]
lib/Bio/DB/Query/GenBank.pm [moved from Bio/DB/Query/GenBank.pm with 100% similarity]
lib/Bio/DB/Query/WebQuery.pm [moved from Bio/DB/Query/WebQuery.pm with 100% similarity]
lib/Bio/DB/QueryI.pm [moved from Bio/DB/QueryI.pm with 100% similarity]
lib/Bio/DB/RandomAccessI.pm [moved from Bio/DB/RandomAccessI.pm with 100% similarity]
lib/Bio/DB/RefSeq.pm [moved from Bio/DB/RefSeq.pm with 100% similarity]
lib/Bio/DB/ReferenceI.pm [moved from Bio/DB/ReferenceI.pm with 100% similarity]
lib/Bio/DB/Registry.pm [moved from Bio/DB/Registry.pm with 100% similarity]
lib/Bio/DB/SeqFeature.pm [moved from Bio/DB/SeqFeature.pm with 100% similarity]
lib/Bio/DB/SeqFeature/NormalizedFeature.pm [moved from Bio/DB/SeqFeature/NormalizedFeature.pm with 100% similarity]
lib/Bio/DB/SeqFeature/NormalizedFeatureI.pm [moved from Bio/DB/SeqFeature/NormalizedFeatureI.pm with 100% similarity]
lib/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm [moved from Bio/DB/SeqFeature/NormalizedTableFeatureI.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Segment.pm [moved from Bio/DB/SeqFeature/Segment.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Store.pm [moved from Bio/DB/SeqFeature/Store.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Store/DBI/Iterator.pm [moved from Bio/DB/SeqFeature/Store/DBI/Iterator.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Store/DBI/Pg.pm [moved from Bio/DB/SeqFeature/Store/DBI/Pg.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Store/DBI/SQLite.pm [moved from Bio/DB/SeqFeature/Store/DBI/SQLite.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Store/DBI/mysql.pm [moved from Bio/DB/SeqFeature/Store/DBI/mysql.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm [moved from Bio/DB/SeqFeature/Store/FeatureFileLoader.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Store/GFF2Loader.pm [moved from Bio/DB/SeqFeature/Store/GFF2Loader.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm [moved from Bio/DB/SeqFeature/Store/GFF3Loader.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Store/LoadHelper.pm [moved from Bio/DB/SeqFeature/Store/LoadHelper.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Store/Loader.pm [moved from Bio/DB/SeqFeature/Store/Loader.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Store/bdb.pm [moved from Bio/DB/SeqFeature/Store/bdb.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Store/berkeleydb.pm [moved from Bio/DB/SeqFeature/Store/berkeleydb.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Store/berkeleydb3.pm [moved from Bio/DB/SeqFeature/Store/berkeleydb3.pm with 100% similarity]
lib/Bio/DB/SeqFeature/Store/memory.pm [moved from Bio/DB/SeqFeature/Store/memory.pm with 100% similarity]
lib/Bio/DB/SeqI.pm [moved from Bio/DB/SeqI.pm with 100% similarity]
lib/Bio/DB/SeqVersion.pm [moved from Bio/DB/SeqVersion.pm with 100% similarity]
lib/Bio/DB/SeqVersion/gi.pm [moved from Bio/DB/SeqVersion/gi.pm with 100% similarity]
lib/Bio/DB/SwissProt.pm [moved from Bio/DB/SwissProt.pm with 100% similarity]
lib/Bio/DB/Taxonomy.pm [moved from Bio/DB/Taxonomy.pm with 100% similarity]
lib/Bio/DB/Taxonomy/entrez.pm [moved from Bio/DB/Taxonomy/entrez.pm with 100% similarity]
lib/Bio/DB/Taxonomy/flatfile.pm [moved from Bio/DB/Taxonomy/flatfile.pm with 100% similarity]
lib/Bio/DB/Taxonomy/greengenes.pm [moved from Bio/DB/Taxonomy/greengenes.pm with 100% similarity]
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lib/Bio/DB/Taxonomy/sqlite.pm [moved from Bio/DB/Taxonomy/sqlite.pm with 100% similarity]
lib/Bio/DB/UpdateableSeqI.pm [moved from Bio/DB/UpdateableSeqI.pm with 100% similarity]
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lib/Bio/Index/Fasta.pm [moved from Bio/Index/Fasta.pm with 100% similarity]
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lib/Bio/LiveSeq/Repeat_Region.pm [moved from Bio/LiveSeq/Repeat_Region.pm with 100% similarity]
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lib/Bio/Matrix/PSM/SiteMatrix.pm [moved from Bio/Matrix/PSM/SiteMatrix.pm with 100% similarity]
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lib/Bio/Matrix/PhylipDist.pm [moved from Bio/Matrix/PhylipDist.pm with 100% similarity]
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lib/Bio/Ontology/DocumentRegistry.pm [moved from Bio/Ontology/DocumentRegistry.pm with 100% similarity]
lib/Bio/Ontology/GOterm.pm [moved from Bio/Ontology/GOterm.pm with 100% similarity]
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lib/Bio/Ontology/OBOEngine.pm [moved from Bio/Ontology/OBOEngine.pm with 100% similarity]
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lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm [moved from Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm with 100% similarity]
lib/Bio/Ontology/SimpleOntologyEngine.pm [moved from Bio/Ontology/SimpleOntologyEngine.pm with 100% similarity]
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lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm [moved from Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm with 100% similarity]
lib/Bio/OntologyIO/InterProParser.pm [moved from Bio/OntologyIO/InterProParser.pm with 100% similarity]
lib/Bio/OntologyIO/dagflat.pm [moved from Bio/OntologyIO/dagflat.pm with 100% similarity]
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lib/Bio/Search/HSP/BlastPullHSP.pm [moved from Bio/Search/HSP/BlastPullHSP.pm with 100% similarity]
lib/Bio/Search/HSP/FastaHSP.pm [moved from Bio/Search/HSP/FastaHSP.pm with 100% similarity]
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lib/Bio/Variation/AAChange.pm [moved from Bio/Variation/AAChange.pm with 100% similarity]
lib/Bio/Variation/AAReverseMutate.pm [moved from Bio/Variation/AAReverseMutate.pm with 100% similarity]
lib/Bio/Variation/Allele.pm [moved from Bio/Variation/Allele.pm with 100% similarity]
lib/Bio/Variation/DNAMutation.pm [moved from Bio/Variation/DNAMutation.pm with 100% similarity]
lib/Bio/Variation/IO.pm [moved from Bio/Variation/IO.pm with 100% similarity]
lib/Bio/Variation/IO/flat.pm [moved from Bio/Variation/IO/flat.pm with 100% similarity]
lib/Bio/Variation/IO/xml.pm [moved from Bio/Variation/IO/xml.pm with 100% similarity]
lib/Bio/Variation/README [moved from Bio/Variation/README with 100% similarity]
lib/Bio/Variation/RNAChange.pm [moved from Bio/Variation/RNAChange.pm with 100% similarity]
lib/Bio/Variation/SNP.pm [moved from Bio/Variation/SNP.pm with 100% similarity]
lib/Bio/Variation/SeqDiff.pm [moved from Bio/Variation/SeqDiff.pm with 100% similarity]
lib/Bio/Variation/VariantI.pm [moved from Bio/Variation/VariantI.pm with 100% similarity]
lib/Bio/WebAgent.pm [moved from Bio/WebAgent.pm with 100% similarity]
lib/BioPerl.pm [moved from BioPerl.pm with 100% similarity]
scripts/Bio-DB-GFF/README [deleted file]
scripts/DB/TAG [deleted file]
scripts/README [deleted file]
scripts/das/README [deleted file]
scripts/das/TAG [deleted file]
scripts/index/TAG [deleted file]
scripts/searchio/README [deleted file]
scripts/searchio/TAG [deleted file]
scripts/seq/TAG [deleted file]
scripts/seqstats/TAG [deleted file]
scripts/taxa/TAG [deleted file]
scripts/tree/TAG [deleted file]
scripts/utilities/README [deleted file]
scripts/utilities/TAG [deleted file]
t/PodSyntax.t [deleted file]