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|
bin/addcascades
bin/AutoDBI.PL
bin/chado-build-schema.pl
bin/chado-fix-flybase-instance.pl
bin/config.PLS
bin/create-bridge-sql.pl
bin/create-so-bridge.pl
bin/gencode2sql.pl
bin/gmod_add_organism.pl
bin/gmod_apollo_triggers.pl
bin/gmod_bulk_load_pubmed.pl
bin/gmod_bulkfiles.pl
bin/gmod_chado_properties.pl
bin/gmod_dump_gff3.pl
bin/gmod_extract_dbxref_from_gff.pl
bin/gmod_fasta2gff3.pl
bin/gmod_gff2biomart5.pl
bin/gmod_gff3_preprocessor.pl
bin/gmod_load_cvterms.pl
bin/gmod_make_cvtermpath.pl
bin/gmod_make_gff_from_dbxref.pl
bin/gmod_materialized_view_tool.pl
bin/gmod_sort_gff3.pl
bin/gmod_update_chado.pl
bin/interactions2SIF.pl
bin/load_ncbi_taxonomy.pl
bin/load_taxonomy_cvterms.pl
bin/make_cvtermpath.pl
bin/make_cvtermpath.sh
bin/make_partial_indexes.pl
bin/pg2cdbi.pl
bin/pg2cdbi_viaTT.pl
bin/pg2diagram.pl
bin/pg2graphviz.pl
bin/pg2graphviz_svg.pl
bin/pg2html.pl
bin/privileges.tmpl
bin/Skip_tables.pm
bin/test_load.pl
bin/test_load.sh
bin/ucsc_genes2gff.pl
bin/ucsc_snp2gff.pl
chado-module-metadata.xml
chado-xml/examples/CG10833.expanded.chado-xml
chado-xml/examples/CG10833.with-macros.chado-xml
chado-xml/examples/CG10833.with-macros.defaults-stripped.chado-xml
chado-xml/README
chado-xml/xsl/chado-create-feature-nesting.xsl
chado-xml/xsl/chado-expand-macros.xsl
chado-xml/xsl/chado-insert-macros.xsl
chado-xml/xsl/chado-remove-analysis-features.xsl
chado-xml/xsl/chado-remove-default-elements.xsl
chado-xml/xsl/chado-remove-feature-nesting.xsl
chado-xml/xsl/README
Changes
Changes.GMOD
Changes.sql
conf/bulkfiles/anogam.xml
conf/bulkfiles/blastfiles.xml
conf/bulkfiles/bulkfiles_template.xml
conf/bulkfiles/chadofeatconv.xml
conf/bulkfiles/chadofeatsql.xml
conf/bulkfiles/chadogenepagesql.xml
conf/bulkfiles/dmelhetfeatconv.xml
conf/bulkfiles/dmelr420.xml
conf/bulkfiles/dmelr430.xml
conf/bulkfiles/dpsebulk-p4.xml
conf/bulkfiles/dpsebulk-p5.xml
conf/bulkfiles/dpsebulk-r2.xml
conf/bulkfiles/drosmelgb.xml
conf/bulkfiles/fastawriter.xml
conf/bulkfiles/fbbulk-hetr3.xml
conf/bulkfiles/fbbulk-r3.xml
conf/bulkfiles/fbbulk-r3h.xml
conf/bulkfiles/fbbulk-r4.xml
conf/bulkfiles/fbbulk-r41.xml
conf/bulkfiles/fbbulk-r411.xml
conf/bulkfiles/fbreleases.xml
conf/bulkfiles/featuresets.xml
conf/bulkfiles/filesets.xml
conf/bulkfiles/gbrowseconf.xml
conf/bulkfiles/gbrowseconf_fb.xml
conf/bulkfiles/genbanksubmit.xml
conf/bulkfiles/genomeweb.xml
conf/bulkfiles/organisms.xml
conf/bulkfiles/sgdbulk.xml
conf/bulkfiles/sgdbulk1.xml
conf/bulkfiles/sgdfeatconf.xml
conf/bulkfiles/site_defaults.xml
conf/bulkfiles/site_eugenes_defaults.xml
conf/bulkfiles/spbase.xml
conf/bulkfiles/spbasefeatconf.xml
conf/bulkfiles/tablewriter.xml
conf/bulkfiles/toacode.xml
conf/bulkfiles/tognomap.xml
conf/chado2apollo-apache.conf
doc/about-gff2biomart.pod
doc/COPYRIGHT
doc/css/chado.css
doc/examples/dicistronic-gene-example.chado
doc/examples/dicistronic-gene-example.chaos
doc/examples/dicistronic-gene-example.game
doc/examples/dicistronic-gene-example.png
doc/examples/dmel_NPFR1.chado
doc/examples/dmel_NPFR1.chaos
doc/examples/dmel_NPFR1.game
doc/examples/dmel_NPFR1.png
doc/gff2biomart-update.note
doc/gmod-tools-readme.pod
doc/index.html
doc/wiki/generateChadoWikiTables.py
doc/wiki/wiki.tmpl
doc/xsl/scenario-to-html-inline.xsl
doc/xsl/scenario-to-html.xsl
INSTALL.Chado
INSTALL.Custom
install_util/conf_install.PLS
install_util/install.pm
install_util/src_install.PLS
lib/Bio/Chado/Builder.pm
lib/Bio/Chado/Config.pm
lib/Bio/FeatureIO/chado.pm
lib/Bio/FeatureIO/chadobulk.pm
lib/Bio/GMOD/Bulkfiles.pm
lib/Bio/GMOD/Bulkfiles/AcodeWriter.pm
lib/Bio/GMOD/Bulkfiles/BlastWriter.pm
lib/Bio/GMOD/Bulkfiles/BulkWriter.pm
lib/Bio/GMOD/Bulkfiles/FastaWriter.pm
lib/Bio/GMOD/Bulkfiles/FeatureWriter.pm
lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm
lib/Bio/GMOD/Bulkfiles/GnomapWriter.pm
lib/Bio/GMOD/Bulkfiles/MyLargePrimarySeq.pm
lib/Bio/GMOD/Bulkfiles/MySplitLocation.pm
lib/Bio/GMOD/Bulkfiles/SWISS_CRC64.pm
lib/Bio/GMOD/Bulkfiles/TableWriter.pm
lib/Bio/GMOD/Config.pm
lib/Bio/GMOD/Config2.pm
lib/Bio/GMOD/DB/Adapter.pm
lib/Bio/GMOD/DB/Adapter/FeatureIterator.pm
lib/Bio/GMOD/DB/Adapter/Wormbase.pm
lib/Bio/GMOD/DB/Config.pm
lib/Bio/GMOD/DB/Tools/ETA.pm
lib/Bio/GMOD/Load.pm
lib/Bio/GMOD/Load/GFF.pm
lib/Bio/GMOD/SeqUtils.pm
LICENSE
load/bin/bulk_load_gff3.PLS
load/bin/load_gff3.PLS
load/Build.PL
load/etc/chap.obo
load/etc/extra.sql
load/etc/feature_property.obo
load/etc/genbank_feature_property.obo
load/etc/initialize.sql
load/etc/README
load/tt2/load.conf.tt2
Makefile.PL
MANIFEST This list of files
MANIFEST.SKIP
modules/audit/add-audits.tmpl
modules/audit/audit_tables.sql
modules/audit/make_audit_ddl
modules/bin/makedep.pl
modules/bin/mk.pl
modules/cell_line/cell_line.html
modules/cell_line/cell_line.sql
modules/companalysis/companalysis.html
modules/companalysis/companalysis.sql
modules/companalysis/functions/companalysis-loading.plpgsql
modules/companalysis/functions/companalysis-loading.sqlapi
modules/contact/contact.html
modules/contact/contact.sql
modules/contact/contactprop.sql
modules/cv/bridges/bin/create-bridge-sql.pl
modules/cv/bridges/godb-bridge.plpgsql
modules/cv/bridges/godb-bridge.sql.xml
modules/cv/cv-dbapi.sqli
modules/cv/cv.html
modules/cv/cv.sql
modules/cv/functions/cv-helper.plpgsql
modules/cv/functions/cv-helper.sqlapi
modules/cv/functions/deductive_closure.plpgsql
modules/cv/functions/deductive_closure.sqlapi
modules/cv/functions/detect_cycle.plpgsql
modules/cv/functions/fill_cvtermpath.plpgsql
modules/cv/functions/get_subj_obj_ids.plpgsql
modules/cv/views/cv-convenience-views.sql
modules/cv/views/cv-logical-definitions-views.sql
modules/cv/views/cv-report.sql
modules/cv/views/cv-stats.sql
modules/cv/views/cv-views.sql
modules/default_nofuncs.sql
modules/default_schema.sql
modules/expression/expression.html
modules/expression/expression.sql
modules/extension.modules
modules/function.modules
modules/general/functions/general-loading.plpgsql
modules/general/functions/general-loading.sqlapi
modules/general/general.html
modules/general/general.sql
modules/general/views/general-report.sql
modules/genetic/genetic.html
modules/genetic/genetic.sql
modules/idb-full.modules
modules/library/library.html
modules/library/library.sql
modules/mage/mage.html
modules/mage/mage.sql
modules/mage/mage.views
modules/map/map.html
modules/map/map.sql
modules/module-tables.json
modules/natural_diversity/natural_diversity.html
modules/natural_diversity/natural_diversity.sql
modules/nofuncs.html
modules/nofuncs.sql
modules/organism/examples/examples-orgs.chado-xml
modules/organism/functions/organism-loading.plpgsql
modules/organism/functions/organism.plpgsql
modules/organism/functions/organism.sqlapi
modules/organism/organism.html
modules/organism/organism.sql
modules/phenotype/phenotype.html
modules/phenotype/phenotype.sql
modules/phylogeny/Changes
modules/phylogeny/examples/org.chado-xml
modules/phylogeny/examples/README
modules/phylogeny/examples/sample-phylo.chado-xml
modules/phylogeny/examples/sample-phylo.nhx
modules/phylogeny/functions/phylo.plpgsql
modules/phylogeny/functions/phylo.sqlapi
modules/phylogeny/phylogeny.html
modules/phylogeny/phylogeny.sql
modules/project/project.html
modules/project/project.sql
modules/pub/pub.html
modules/pub/pub.sql
modules/sequence/apollo-bridge/ad_hoc_cv
modules/sequence/apollo-bridge/apollo-triggers.plpgsql
modules/sequence/apollo-bridge/apollo.inserts
modules/sequence/apollo-bridge/cv_inserts.sql
modules/sequence/apollo-bridge/insert_ad_doc_cv.pl
modules/sequence/apollo-bridge/naming_rules.txt
modules/sequence/apollo-bridge/sample_db/README
modules/sequence/bdgp/bdgp-indexes.sql
modules/sequence/bdgp/bdgp-views.sql
modules/sequence/bdgp/bin/create-so-layer.pl
modules/sequence/bdgp/doc/chado-sequence-ontology-layer.sxi
modules/sequence/bdgp/populate-match-floc.sql
modules/sequence/bdgp/README
modules/sequence/bdgp/so-views.sql
modules/sequence/bridges/bin/create-sofa-bridge.pl
modules/sequence/bridges/chaos-bridge.sql.xml
modules/sequence/bridges/gadfly-bridge.sql.xml
modules/sequence/bridges/so-bridge.sql
modules/sequence/bridges/sofa-bridge.sql
modules/sequence/functions/create_soi.plpgsql
modules/sequence/functions/delete-trigger.plpgsql
modules/sequence/functions/feature.plpgsql
modules/sequence/functions/feature.sqlapi
modules/sequence/functions/feature_ids_fx.plpgsql
modules/sequence/functions/feature_subalignments.plpgsql
modules/sequence/functions/frange.plpgsql
modules/sequence/functions/locgraph.plpgsql
modules/sequence/functions/locgraph.sqlapi
modules/sequence/functions/range.plpgsql
modules/sequence/functions/range.sqlapi
modules/sequence/functions/sequence-cv-helper.plpgsql
modules/sequence/functions/sequence-cv-helper.sqlapi
modules/sequence/functions/sequence-loading.plpgsql
modules/sequence/functions/sequence-loading.sqlapi
modules/sequence/functions/sequtil.plpgsql
modules/sequence/functions/sequtil.sqlapi
modules/sequence/functions/subsequence.plpgsql
modules/sequence/functions/subsequence.sqlapi
modules/sequence/gencode/gencode.sql
modules/sequence/gencode/gencode_data.sql
modules/sequence/gff-bridge/sequence-gff-funcs.plpgsql
modules/sequence/gff-bridge/sequence-gff-views.sql
modules/sequence/sequence-dbapi.sqli
modules/sequence/sequence.html
modules/sequence/sequence.pgfunc
modules/sequence/sequence.sql
modules/sequence/sequence_opt.xml
modules/sequence/sequence_views.sql
modules/sequence/views/exon-views.sql
modules/sequence/views/implicit-feature-views.sql
modules/sequence/views/range-views.sql
modules/sequence/views/sequence-cv-views.sql
modules/sequence/views/sequence-report.sql
modules/stock/stock.html
modules/stock/stock.sql
README
README.Apollo
schemas/1-1.1/diff.sql
schemas/1-1.11/diff.sql
schemas/1-1.2/diff.sql
schemas/1.1-1.2/diff.sql
schemas/1.1/default_schema.sql
schemas/1.11-1.2/diff.sql
schemas/1.11/default_schema.sql
schemas/1.2/default_schema.sql
schemas/1/default_schema.sql
soi/cgi/get_xml.pl
soi/README
soi/scripts/dump_fasta.pl
soi/scripts/dump_segment.pl
soi/scripts/generegion.pl
soi/SOI/Adapter.pm
soi/SOI/Feature.pm
soi/SOI/FeatureDecor.pm
soi/SOI/GAMEHandler.pm
soi/SOI/GFF3Parser.pm
soi/SOI/IntersectGraph.pm
soi/SOI/Outputter.pm
soi/SOI/SOIHandler.pm
soi/SOI/Visitor.pm
soi/t/data/AE003790.cDNA.game.xml
soi/t/data/AE003790.soi.xml
soi/t/t_soi_parse_intersect
soi/templates/features_by_name.soi
soi/templates/genes_by_child_count.soi
soi/templates/genes_by_GO_term.soi
soi/templates/top_typed_feature.soi
soi/templates/top_typed_feature_no_soi.soi
soi/templates/typed_genes.soi
stag-templates/chado-basicfeature.stg
stag-templates/chado-cvterm.stg
stag-templates/chado-cvtermgraph.stg
stag-templates/chado-feature-by-direct-cvterm.stg
stag-templates/chado-feature_children.stg
stag-templates/chado-feature_relationship.stg
stag-templates/chado-feature_synonym.stg
stag-templates/chado-genemodel-with-featureloc.stg
stag-templates/chado-genemodel.stg
stag-templates/chado-mrna.stg
stag-templates/chado-pcgenemodel.stg
stag-templates/chado-protein.stg
stag-templates/chado-roi.stg
stag-templates/chado-upstream-of-alignment.stg
stag-templates/make-publish
stag-templates/README
TODO
UPGRADE.txt
schemas/1-1.21/diff.sql
schemas/1.1-1.21/diff.sql
schemas/1.11-1.21/diff.sql
schemas/1.2-1.21/diff.sql
#the following added by generate_diff_dirs.pl
schemas/1-1.22/diff.sql
schemas/1.1-1.22/diff.sql
schemas/1.11-1.22/diff.sql
schemas/1.2-1.22/diff.sql
schemas/1.21-1.22/diff.sql
META.yml Module meta-data (added by MakeMaker)
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