Differences

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--- chado [2010/01/13 09:14] – 172.26.15.184
+++ chado [2010/01/14 08:12] – 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>
-''psql tparvadb''
+Create pgsql database.
- ''chado> SELECT * FROM organism;''
- ''chado> INSERT INTO organism ( abbreviation, genus, species, common_name) VALUES ('T.testus','Test','testus','test');''
+<code>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''
+chado> \q</code>
+Load gff3 data into database
-''gmod_bulk_load_gff3.pl  --dbname tparvadb --dbxref GeneID --organism T.parva --gff T.parva_chr1.gb.gff''
+<code>gmod_bulk_load_gff3.pl  --dbname tparvadb --dbxref GeneID --organism T.parva --gff T.parva_chr1.gb.gff</code>