1659b2691cac2372abde8c569916fc294aa9a56c
braney
  Wed Aug 14 10:32:41 2019 -0700
new go database

diff --git src/hg/makeDb/doc/go.txt src/hg/makeDb/doc/go.txt
index de83377..b6924af 100644
--- src/hg/makeDb/doc/go.txt
+++ src/hg/makeDb/doc/go.txt
@@ -1,255 +1,295 @@
 ### UPDATE GO DATABASE (DONE 04-11-24)
 # Adopted from an earlier process Gill did for his private go database
 # Update GO database (2005-07-26, hartera)
 # Download the terms and make the database.
 
 # Added symlink for the build dir:  /cluster/data/geneOntology
 # so store1 doesn't need to be directly referenced (2007-01-10 kate)
 
     ssh hgwdev
         
     mkdir /cluster/data/geneOntology/20041124
     cd /cluster/data/geneOntology/20041124
 
     wget --timestamping http://www.godatabase.org/dev/database/archive/latest/go_200411-assocdb-data.gz
 
     hgsql mysql <<end
     create database go041124;
     end
     zcat go_*data.gz | hgsql go041124
 
 # Download the associations
     wget --timestamping ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.goa_uniprot.gz
 
 # Note no specific taxon specified, this will import everything
     zcat gene_association.goa_uniprot.gz | hgGoAssociation go041124 goaPart stdin 
 # Passed 4502016 of 5291097 of 5291097, 85.09%
 
 # Ask sys-admin to point go to go041124
 
 # Asked sys-admin to rename database to go041115 and point go to the new name -- kuhn 12-06-04
 
 # REBUILD GO WITH LATEST VERSION (DONE, 2005-07-26, hartera)
 # Re-made GO database as above, only the dates in names have changed
 # so downloads are in /cluster/store1/geneOntology/20050726 and the database
 # is called go050726. 
 # Download file of terms is go_200507-assocdb-data.gz (July 18, 2005)
 # Download file of associations is gene_association.goa_uniprot.gz 
 # (June 16, 2005)
 # hgGoAssociation:
 # Passed 5515470 of 6413534 of 6413534, 86.00% 
 ##########################################################################
 # UPDATE GO DATABASE (DONE, 2006-12-20, Fan)
 
 # UPDATE GO DATABASE
 # Download the terms and make the database.
 ssh hgwdev
 mkdir /cluster/store1/geneOntology/20061219
 cd /cluster/store1/geneOntology/20061219
 
 wget --timestamping
 http://www.godatabase.org/dev/database/archive/latest/go_200612-assocdb-data.gz
 
 hgsql mysql <<end
 create database go061219;
 end
 zcat go_*data.gz | sed -e 's/ENGINE=MyISAM DEFAULT
 CHARSET=latin1/TYPE=MyISAM/g' >j.tmp
 hgsql go061219 <j.tmp
 rm j.tmp
 
 wget --timestamping
 ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.goa_uniprot.gz
 
 # The format of gene_association.goa_uniprot.gz changed, there is comment
 # lines at the head now.
 # Updated hgGoAssociation.c to skip those initial comment lines.
 
 zcat gene_association.goa_uniprot.gz\
 |/cluster/home/fanhsu/bin/x86_64/hgGoAssociation go061219 goaPart stdin
 # Passed 9049274 of 10512956 of 10512956, 86.08%
 
 # Ask sys-admin to switch the database pointer go to point to go061219.
 ##########################################################################
 ### UPDATE GO DATABASE (DONE 07-01-16, Fan)
 
 # UPDATE GO DATABASE
 # Download the terms and make the database.
 ssh hgwdev
 mkdir /cluster/store1/geneOntology/20070111
 cd /cluster/store1/geneOntology/20070111
 
 wget --timestamping \
 http://www.godatabase.org/dev/database/archive/latest/go_200701-assocdb-data.gz
 
 hgsql mysql -e 'create database go070111'
 
 zcat go_*data.gz | sed -e 's/ENGINE=MyISAM DEFAULT CHARSET=latin1/TYPE=MyISAM/g' >j.tmp
 hgsql go070111 <j.tmp
 rm j.tmp
 
 # Please note the new place to get gene_association.goa_uniprot.gz
 wget --timestamping \
 ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz
 
 zcat gene_association.goa_uniprot.gz\
 |hgGoAssociation go070111 goaPart stdin
 
 # Passed 10341476 of 12083865 of 12083865, 85.58%
 
 # angie suggests running this at the end (it only make goaPart.as):
 # makeTableDescriptions go hg/lib/goaPart.as (BK 2007-07-05)
 
 # Ask sys-admin to switch the database pointer go to point to go061219.
 
 ##########################################################################
 ### UPDATE GO DATABASE (DONE 1/30/08, Fan)
 
 # UPDATE GO DATABASE
 # Download the terms and make the database.
 ssh hgwdev
 mkdir /cluster/store1/geneOntology/20080130
 cd /cluster/store1/geneOntology/20080130
 
 wget --timestamping
 http://archive.geneontology.org/latest/go_200801-assocdb-data.gz
 
 hgsql mysql -e 'create database go080130'
 
 zcat go_*data.gz | sed -e 's/ENGINE=MyISAM DEFAULT CHARSET=latin1/TYPE=MyISAM/g' >j.tmp
 hgsql go080130 <j.tmp
 rm j.tmp
 
 # Please note the new place to get gene_association.goa_uniprot.gz
 wget --timestamping \
 ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz
 
 zcat gene_association.goa_uniprot.gz\
 |hgGoAssociation go080130 goaPart stdin
 
 Passed 16890026 of 25763098 of 25763098, 65.56%
 
 # Ask sys-admin to switch the database pointer go to point to go080130.
 ##########################################################################
 ### UPDATE GO DATABASE (DONE 2014-02-23 braney)
 
 # UPDATE GO DATABASE
 # Download the terms and make the database.
 ssh hgwdev
 mkdir /hive/data/outside/geneOntology/20150121
 cd  /hive/data/outside/geneOntology/20150121
 
 wget "http://archive.geneontology.org/full/2015-01-01/go_201501-assocdb-tables.tar.gz"
 
 hgsql -e 'create database go150121'
 tar xvfz go_201501-assocdb-tables.tar.gz
 
 cd go_201402-assocdb-tables
 for i in *.txt
 do
     if test -s $i
     then
 	cat `basename  $i .txt`.sql
     fi
 done | hgsql go140213
 
 for i in *.txt
 do 
     if test -s $i
     then
 	echo $i
 	echo "load data local infile '$i' into table `basename $i .txt`" | hgsql go140213
     fi
 done
 
 # Please note the new place to get gene_association.goa_uniprot.gz
 wget --timestamping \
 ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz
 
 zcat gene_association.goa_uniprot.gz |hgGoAssociation go140213 goaPart stdin
 
 # Passed 192715679 of 254966113 of 254966113, 75.58%
 
 # Ask sys-admin to switch the database pointer go to point to go140213
 ##########################################################################
 ### UPDATE GO DATABASE (DONE 2015-01-21 braney)
 
 # UPDATE GO DATABASE
 # Download the terms and make the database.
 ssh hgwdev
 mkdir /hive/data/outside/geneOntology/20150121
 cd  /hive/data/outside/geneOntology/20150121
 
 wget "http://archive.geneontology.org/full/2015-01-01/go_201501-assocdb-tables.tar.gz"
 
 hgsql -e 'create database go150121'
 tar xvfz go_201501-assocdb-tables.tar.gz
 
 cd go_201501-assocdb-tables
 for i in *.txt
 do
     if test -s $i
     then
 	cat `basename  $i .txt`.sql
     fi
 done | hgsql go150121
 
 for i in *.txt
 do 
     if test -s $i
     then
 	echo $i
 	echo "load data local infile '$i' into table `basename $i .txt`" | hgsql go150121
     fi
 done
 
 # Please note the new place to get gene_association.goa_uniprot.gz
 wget --timestamping \
 ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz
 
 zcat gene_association.goa_uniprot.gz |hgGoAssociation go150121 goaPart stdin
 # Passed 300033664 of 401499085 of 401499085, 74.73%
 
 # Ask sys-admin to switch the database pointer go to point to go150121
 
 ##########################################################################
 ### UPDATE GO DATABASE (DONE 2018-04-26 braney)
 
 # UPDATE GO DATABASE
 # Download the terms and make the database.
 ssh hgwdev
 mkdir /hive/data/outside/geneOntology/20180426
 cd  /hive/data/outside/geneOntology/20180426
 
 #wget "http://archive.geneontology.org/full/2015-01-01/go_201501-assocdb-tables.tar.gz"
 wget "http://archive.geneontology.org/full/2017-01-01/go_monthly-assocdb-tables.tar.gz"
 
 hgsql -e 'create database go180426'
 tar xvfz go_monthly-assocdb-tables.tar.gz
 
 cd go_monthly-assocdb-tables
 for i in *.txt
 do
     if test -s $i
     then
 	cat `basename  $i .txt`.sql
     fi
 done | hgsql go180426
 
 for i in *.txt
 do 
     if test -s $i
     then
 	echo $i
 	echo "load data local infile '$i' into table `basename $i .txt`" | hgsql go180426
     fi
 done
 
 # Please note the new place to get gene_association.goa_uniprot.gz
 wget --timestamping \
 ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz
 
 zcat goa_uniprot_all.gaf.gz |hgGoAssociation go180426 goaPart stdin
 # Passed 378374005 of 508539120 of 508539120, 74.40%
 
 # Ask sys-admin to switch the database pointer go to point to go140213
+##########################################################################
+### UPDATE GO DATABASE (DONE 2019-08-14 braney)
+
+# UPDATE GO DATABASE
+# Download the terms and make the database.
+ssh hgwdev
+mkdir /hive/data/outside/geneOntology/20190809
+cd  /hive/data/outside/geneOntology/20190809
+
+#wget "http://archive.geneontology.org/full/2015-01-01/go_201501-assocdb-tables.tar.gz"
+wget "http://archive.geneontology.org/full/2017-01-01/go_monthly-assocdb-tables.tar.gz"
+
+hgsql -e 'create database go190809'
+tar xvfz go_monthly-assocdb-tables.tar.gz
+
+cd go_monthly-assocdb-tables
+for i in *.txt
+do
+    if test -s $i
+    then
+	cat `basename  $i .txt`.sql
+    fi
+done | hgsql go190809
+
+for i in *.txt
+do 
+    if test -s $i
+    then
+	echo $i
+	echo "load data local infile '$i' into table `basename $i .txt`" | hgsql go190809
+    fi
+done
+
+wget --timestamping \
+ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz
+
+zcat goa_uniprot_all.gaf.gz |hgGoAssociation go190809 goaPart stdin
+#Passed 527292541 of 697908155 of 697908155, 75.55%
+
+# Ask sys-admin to switch the database pointer go to point to go190809