From 82d8f9ea49d7345d39dc3d89c626691940ca7b53 Mon Sep 17 00:00:00 2001 From: preecej Date: Wed, 26 Oct 2011 21:45:24 +0000 Subject: [PATCH] Cleanup... svn path=/; revision=199 --- .../ara_rice_exclusive_sets.pl | 0 .../convert_bad_pub_authors_to_years.pl | 0 .../convert_bad_step_interaction_datatypes.pl | 0 .../perl_singletons/pathway_gene_swapper.pl | 0 .../reactome_chebi_mapping.pl | 0 .../zea_Maize_PO_CoGe_name_swap.pl | 0 .../php_singletons/PO_web_service.php | 0 .../preecej}/php_singletons/cmd_line_test.php | 0 ...actome_EC_number_reaction_name_mapping.sql | 32 ++++++++++++++++++ planteome/.gitignore | 0 .../paw}/content_pages/Main_Page.wiki | 0 .../content_pages/Reference:Plant_Taxa.wiki | 0 .../paw}/extensions/DataTransfer_PS/COPYING | 0 .../DataTransfer_PS/DataTransfer.php | 0 .../paw}/extensions/DataTransfer_PS/INSTALL | 0 .../paw}/extensions/DataTransfer_PS/README | 0 .../data_transfer_0.3.8.tar.gz | Bin .../DataTransfer_PS/includes/DT_ImportJob.php | 0 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a/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl b/Personnel/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl similarity index 100% rename from preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl rename to Personnel/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl diff --git a/preecej/perl_singletons/zea_Maize_PO_CoGe_name_swap.pl b/Personnel/preecej/perl_singletons/zea_Maize_PO_CoGe_name_swap.pl similarity index 100% rename from preecej/perl_singletons/zea_Maize_PO_CoGe_name_swap.pl rename to Personnel/preecej/perl_singletons/zea_Maize_PO_CoGe_name_swap.pl diff --git a/preecej/php_singletons/PO_web_service.php b/Personnel/preecej/php_singletons/PO_web_service.php similarity index 100% rename from preecej/php_singletons/PO_web_service.php rename to Personnel/preecej/php_singletons/PO_web_service.php diff --git a/preecej/php_singletons/cmd_line_test.php b/Personnel/preecej/php_singletons/cmd_line_test.php similarity index 100% rename from preecej/php_singletons/cmd_line_test.php rename to Personnel/preecej/php_singletons/cmd_line_test.php diff --git a/Personnel/preecej/sql_scripts/Reactome_EC_number_reaction_name_mapping.sql b/Personnel/preecej/sql_scripts/Reactome_EC_number_reaction_name_mapping.sql new file mode 100644 index 0000000..6f60c73 --- /dev/null +++ b/Personnel/preecej/sql_scripts/Reactome_EC_number_reaction_name_mapping.sql @@ -0,0 +1,32 @@ +use gk_central_042211; +/* query to id fully-qualified EC numbers in poorly-named A.th. reactions */ +select e2n.name, d.identifier from ReactionlikeEvent r +join Event_2_crossReference e2c on e2c.DB_ID = r.DB_ID +join Event_2_name e2n on e2n.DB_ID = r.DB_ID +join DatabaseIdentifier d on d.DB_ID = e2c.crossReference +join Event_2_species e on e.DB_ID = r.DB_ID +join Species s on s.DB_ID = e.species +join Taxon_2_name t on t.DB_ID = s.DB_ID +where t.name like 'Arabidopsis%' +and d.referenceDatabase = 4 +and e2n.name like '%->%' +and d.identifier not like '%-%' +order by e2n.name; + +use test; +/* load in PJ's EC nums and names file */ +/* mysqlimport -u root -p -v --local --ignore-lines=12 test ./EC_reaction_names.txt */ + +/* scratch queries */ +select * from Taxon_2_name +where name like '%Ara%'; + +select * from Species s +join Taxon_2_name t on t.DB_ID = s.DB_ID +where t.name like '%Arabi%'; + +select * from Event_2_crossReference; + +select * from DatabaseIdentifier; + +select * from ReferenceDatabase; \ No newline at end of file diff --git a/planteome/.gitignore b/planteome/.gitignore deleted file mode 100644 index e69de29..0000000 diff --git a/preecej/semantic_wiki/content_pages/Main_Page.wiki b/planteome/paw/content_pages/Main_Page.wiki similarity index 100% rename from preecej/semantic_wiki/content_pages/Main_Page.wiki rename to planteome/paw/content_pages/Main_Page.wiki diff --git a/preecej/semantic_wiki/content_pages/Reference:Plant_Taxa.wiki b/planteome/paw/content_pages/Reference:Plant_Taxa.wiki similarity index 100% rename from preecej/semantic_wiki/content_pages/Reference:Plant_Taxa.wiki rename to planteome/paw/content_pages/Reference:Plant_Taxa.wiki diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/COPYING b/planteome/paw/extensions/DataTransfer_PS/COPYING similarity index 100% rename from preecej/semantic_wiki/extensions/DataTransfer_PS/COPYING rename to planteome/paw/extensions/DataTransfer_PS/COPYING diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/DataTransfer.php b/planteome/paw/extensions/DataTransfer_PS/DataTransfer.php similarity index 100% rename from preecej/semantic_wiki/extensions/DataTransfer_PS/DataTransfer.php rename to planteome/paw/extensions/DataTransfer_PS/DataTransfer.php diff --git a/preecej/semantic_wiki/extensions/DataTransfer_PS/INSTALL b/planteome/paw/extensions/DataTransfer_PS/INSTALL similarity index 100% rename from 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