Differences

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--- chado [2010/01/13 09:07] – 172.26.15.184
+++ chado [2010/01/14 08:09] – 172.26.15.184
@@ Line 1: / Line 1: @@
 ====== Chado ======
-createdb --template=chado tparvadb
+Create new T.pava Chr1 Chado database from Chr1 Genbank file. Local version of Genbank file does not work. Downloaded new file from Genbank: NC_001142.gbk
+Convert file to gff using script:
+<code>
+''genbank2gff3.pl''
+<code>
+Create pgsql database and load data:
+''createdb --template=chado tparvadb''
+''psql tparvadb''
+ ''chado> SELECT * FROM organism;''
+ ''chado> INSERT INTO organism ( abbreviation, genus, species, common_name) VALUES ('T.testus','Test','testus','test');''
+ ''chado> \q''
+''gmod_bulk_load_gff3.pl  --dbname tparvadb --dbxref GeneID --organism T.parva --gff T.parva_chr1.gb.gff''
-psql chado
- chado> SELECT * FROM organism;
- chado> INSERT INTO organism ( abbreviation, genus, species, common_name) VALUES ('T.testus','Test','testus','test');
- chado> \q