#!/bin/tcsh -efx

# This file describes how the proteins090821 database was
# built.  See also the sp090821 database doc, which needs
# to be built first.

set kent = ~/kent
# use this if(0) statement to control section of script to run
#	Look for the BRACKET word to find the corresponding endif and exit
if (0) then  # BRACKET
#	this section is completed, look for the corresponding endif
#	to find the next section that is running.

hgsqladmin create proteins101005

cd /hive/data/inside/proteins
mkdir 101005
cd 101005
mkdir build


# Get HGNC data
$kent/src/hg/protein/getHgnc.pl >hgnc.tab

hgsql proteins101005 < $kent/src/hg/lib/hgnc.sql
hgsql proteins101005 -e 'load data local infile "hgnc.tab" into table hgnc ignore 1 lines'
 
pbHgnc 101005   
hgsql proteins101005 < $kent/src/hg/lib/hgncXref.sql
hgsql proteins101005 -e 'load data local infile "hgncXref.tab" into table hgncXref'

# BUILD spXref2 and spXref3 tables.
cd /hive/data/inside/proteins/101005/build

# Create a bioentry table to use as an internal replacement for accession.
# Takes a minute
hgsql sp101005 -e "create table bioentryID (acc char(16) NOT NULL, bioentryID int not null auto_increment, primary key (bioentryID), unique (acc))"
hgsql sp101005 -e "insert into bioentryID (acc) select acc from sp101005.info order by acc"

# get records with HUGL symbol and descriptions
hgsql sp101005 -N -e 'select d.acc, d.val, taxon, id.bioentryID, 2-isCurated, des.val,hx.symbol, hx.description from displayId d, info i, accToTaxon t, bioentryID id, description des, proteins101005.hgncXref hx where  d.acc=t.acc and d.acc=i.acc and d.acc=id.acc and d.acc = id.acc and d.acc=des.acc and hx.uniProt=d.acc ' >spXref3a.tab

# get records with HUGL symbol and descriptions for variant splice proteins
hgsql sp101005 -N -e 'select v.varAcc, v.varAcc, taxon, id.bioentryID, 2-isCurated, des.val,hx.symbol, hx.description from varAcc v, displayId d, info i, accToTaxon t, bioentryID id, description des, proteins101005.hgncXref hx where v.parAcc=d.acc and d.acc=t.acc and d.acc=i.acc and d.acc=id.acc and d.acc = id.acc and d.acc=des.acc and hx.uniProt=d.acc ' >spXref3av.tab

# get all records and set HUGO symbol and description to "" 

hgsql sp101005 -N -e 'select d.acc, d.val, taxon, id.bioentryID, 2-isCurated, des.val,"", "" from displayId d, info i, accToTaxon t, bioentryID id, description des where  d.acc=t.acc and d.acc=i.acc and d.acc=id.acc and d.acc = id.acc and d.acc=des.acc ' >spXref3b.tab

# get all records and set HUGO symbol and description to "" for variant splice proteins 

hgsql sp101005 -N -e 'select v.varAcc, v.varAcc, taxon, id.bioentryID, 2-isCurated, des.val,"", "" from varAcc v, displayId d, info i, accToTaxon t, bioentryID id, description des where v.parAcc=d.acc and  d.acc=t.acc and d.acc=i.acc and d.acc=id.acc and d.acc = id.acc and d.acc=des.acc ' >spXref3bv.tab

# Clean up temp table.
hgsql sp101005 -e "drop table bioentryID"

# collect all data from the resulting 4 files.

cat spXref3a.tab  spXref3b.tab  spXref3av.tab spXref3bv.tab >spXref3.tab

# load into the spXref3 table
hgLoadSqlTab proteins101005 spXref3 $kent/src/hg/lib/spXref3.sql spXref3.tab

# load the same data into a second temp table
hgLoadSqlTab proteins101005 spXref3B $kent/src/hg/lib/spXref3.sql spXref3.tab

# remove records that have empty HUGO symbol, yet other records 
# of the same accession does have non-empty HUGO symbols.
hgsql proteins101005 -e 'delete spXref3 from spXref3, spXref3B where spXref3.accession=spXref3B.accession and spXref3.hugoSymbol="" and spXref3B.hugoSymbol!=""'

# Drop temp table
hgsql proteins101005 -e "drop table spXref3B"


######################################################################
# BUILD spXref2 TABLE 

# This step takes several hours and produces a table of ~100 million lines.
/cluster/home/fanhsu/bin/x86_64/spToSpXref2 101005 >spXref2.tab


# create and load the big spXref2 table
hgsql proteins101005 < $kent/src/hg/lib/spXref2.sql
cd /hive/data/inside/proteins/101005/build
hgsql proteins101005 -e 'load data local infile "spXref2.tab" into table spXref2'

# create the indices, took about 40 minutes for each index. 

hgsql proteins101005 -e 'create index displayID on spXref2(displayID)'
hgsql proteins101005 -e 'create index extAC on spXref2(extAC)'
hgsql proteins101005 -e 'create index accession on spXref2(accession)'


########################################################################
# Build spOrganism table
hgsql sp101005 -N -e 'select d.val, taxon from displayId d, accToTaxon t where d.acc=t.acc ' >spOrganism.tab

hgLoadSqlTab proteins101005 spOrganism $kent/src/hg/lib/spOrganism.sql ./spOrganism.tab

#	Build spSecondaryID table
cd /hive/data/inside/proteins/101005
hgsql -e "select displayId.val, displayId.acc, otherAcc.val from displayId, \
        otherAcc where otherAcc.acc = displayId.acc;" sp101005 \
	| sed -e "1d" > spSecondaryID.tab

hgLoadSqlTab proteins101005 spSecondaryID $kent/src/hg/lib/spSecondaryID.sql ./spSecondaryID.tab

#	Build pfamXref and pfamDesc tables
# First get pfam info into /hive/data/outside/pfam/current/Pfam-A.full.gz somehow.
# Did it this time with
#   wget --timestamping ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz
cd    /hive/data/outside/pfam/current/

gunzip -c Pfam-A.full.gz | pfamXref proteins101005 stdin pfamADesc.tab pfamAXref.tab >pfamXref.log

hgLoadSqlTab proteins101005 pfamDesc $kent/src/hg/lib/pfamDesc.sql pfamADesc.tab
hgLoadSqlTab proteins101005 pfamXref $kent/src/hg/lib/pfamXref.sql pfamAXref.tab

#	Build the pdbSP table, new process using extDbRef data from spXXXXXX

cd /hive/data/inside/proteins/101005

hgsql sp101005 -N -e 'select extAcc1, d.val from extDbRef x, displayId d, extDb where x.acc=d.acc and extDb.val="PDB" and x.extDb=extDb.id'|sort -u >pdbSP.tab

hgLoadSqlTab proteins101005 pdbSP $kent/src/hg/lib/pdbSP.sql pdbSP.tab

#	Build the spDisease table

hgsql -N -e \
'select comment.acc, displayId.val, commentVal.val from comment, commentVal, commentType ct, displayId where comment.commentType=ct.id and ct.val="DISEASE" and commentVal.id=comment.commentVal and displayId.acc=comment.acc;' \
sp101005 > spDisease.tab

hgLoadSqlTab proteins101005 spDisease $kent/src/hg/lib/spDisease.sql spDisease.tab

# create swInterPro table

cd /hive/data/inside/proteins/101005/build
# Fetch interpro file, last time like so:
#  wget --timestamping "ftp://ftp.ebi.ac.uk/pub/databases/interpro/protein2ipr.dat.gz"
gunzip protein2ipr.dat.gz
# rearrange col positioin to match the old format
cut -f 1 protein2ipr.dat >j1
cut -f 2,3 protein2ipr.dat >j23
cut -f 4,5,6 protein2ipr.dat >j456
paste j1 j456 j23 > interProXref.tab
rm j1 j456 j23

hgLoadSqlTab proteins101005 interProXref $kent/src/hg/lib/interProXref.sql ./interProXref.tab

hgsql proteins101005 -N -e 'select accession, interProId from interProXref;'|sort -u >swInterPro.tab
hgLoadSqlTab proteins101005 swInterPro $kent/src/hg/lib/swInterPro.sql ./swInterPro.tab

# BUILD TABLES FOR pbGlobal (PB V1.1).  These tables are used by the Proteome
# Browser.  

cd /hive/data/inside/proteins/101005
mkdir pbGlobal
cd pbGlobal

# Calculate Pi values for all proteins
pbCalPi sp101005 pi101005.tab


hgLoadSqlTab proteins101005 pepPi $kent/src/hg/lib/pepPi.sql ./pi101005.tab

# Build pepMwAa table

hgsql sp101005 -N -e "select acc, molWeight, aaSize from info" >pepMwAa.tab
hgLoadSqlTab proteins101005 pepMwAa $kent/src/hg/lib/pepMwAa.sql ./pepMwAa.tab

cd /hive/data/inside/proteins/101005/pbGlobal
nice pbCalDistGlobal sp101005 proteins101005

# Load the tables

# Calculate global protein property distributions

hgLoadSqlTab proteins101005 pepCCntDist $kent/src/hg/lib/pepCCntDist.sql pepCCntDist.tab
hgLoadSqlTab proteins101005 pepHydroDist $kent/src/hg/lib/pepHydroDist.sql pepHydroDist.tab
hgLoadSqlTab proteins101005 pepIPCntDist $kent/src/hg/lib/pepIPCntDist.sql pepIPCntDist.tab
hgLoadSqlTab proteins101005 pepMolWtDist $kent/src/hg/lib/pepMolWtDist.sql pepMolWtDist.tab
hgLoadSqlTab proteins101005 pepPiDist $kent/src/hg/lib/pepPiDist.sql pepPiDist.tab
hgLoadSqlTab proteins101005 pepResDist $kent/src/hg/lib/pepResDist.sql pepResDist.tab

# Calculate global AA residue distributions

pbCalResStdGlobal 101005

# Load distribution tables:

hgLoadSqlTab proteins101005 pbAnomLimit $kent/src/hg/lib/pbAnomLimit.sql ./pbAnomLimit.tab
hgLoadSqlTab proteins101005 pbResAvgStd  $kent/src/hg/lib/pbResAvgStd.sql ./pbResAvgStd.tab

# Get taxonomy names table from NCBI.

cd /hive/data/inside/proteins/101005
mkdir taxon
cd taxon
wget --timestamping ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip
unzip taxdmp.zip

# Create table taxonNames in proteins101005

# Load from the file names.dmp into taxonNames table.

# hgsql proteins101005 -e 'drop table taxonNames'
hgsql proteins101005 < $kent/src/hg/lib/taxonNames.sql    
hgsql proteins101005 -e 'load data local infile "names.dmp" into table taxonNames fields terminated by "|" enclosed by "\t";'

# Load and edit pbStamp table

cd /hive/data/inside/proteins/101005
hgsql proteins060115 -N -e "select * from pbStamp" > pbStamp.tab

hgLoadSqlTab proteins101005 pbStamp $kent/src/hg/lib/pbStamp.sql ./pbStamp.tab

cd /hive/data/inside/proteins/101005
mkdir alias
cd alias

hgsql proteins101005 -N -e 'select accession, accession,  "uAcc", "2006-01-15" from spXref3' >j1.tmp
hgsql proteins101005 -N -e 'select accession, accession2, "u2Ac", "2006-01-15" from spSecondaryID' >j2.tmp
hgsql proteins101005 -N -e 'select accession, displayID,  "uDis", "2006-01-15" from spXref3' >j3.tmp
hgsql proteins040515 -N -e 'select accession, displayID,  "oDis", "2004-05-15" from spXref3' >j4.tmp
# PLEASE NOTE: proteins041115 was later deleted by Fan when hgwdev mySQL space was at 100%.
# So, use protein040515 instead.

cat j1.tmp j2.tmp j3.tmp j4.tmp >uniProtAlias.tab
rm j1.tmp j2.tmp j3.tmp j4.tmp

hgLoadSqlTab proteins101005 uniProtAlias $kent/src/hg/lib/uniProtAlias.sql ./uniProtAlias.tab
hgsql proteins101005 -e 'create index alias on uniProtAlias(alias)'

hgsql proteins050415 -N -e 'select * from spOldNew' >spOldNew.tab
hgLoadSqlTab proteins101005 spOldNew $kent/src/hg/lib/spOldNew.sql ./spOldNew.tab

hgsql proteins101005 -e 'create index oldDisplayId on spOldNew(oldDisplayId)'
hgsql proteins101005 -e 'create index newDisplayId on spOldNew(newDisplayId)'

# Build spDeleted table

# Download list of deleted accession numbers from UniProt
cd /hive/data/inside/proteins/101005

wget --timestamping ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/docs/delac_tr.txt
cp delac_tr.txt spDeleted.tab

# Edit spDeleted.tab to get rid of other lines except accession numbers

vi spDeleted.tab
hgLoadSqlTab proteins101005 spDeleted $kent/src/hg/lib/spDeleted.sql ./spDeleted.tab

# CREATE spVariant TABLE TO ENABLE UNIPROT VARIANT SPLICE ISOFORM PROCESSING 

hgsql proteins101005 -N -e 'select accession,accession from spXref3' >j1
cat j1 |grep "-" |sed -e 's/-/\t/'|cut -f 1,3 >j2
cat j1 |grep -v "-" >>j3
cat j2 j3 |sort -u >spVariant.tab
rm j1 j2 j3


hgLoadSqlTab proteins101005 spVariant $kent/src/hg/lib/spVariant.sql ./spVariant.tab
hgsql proteins101005 -e 'create index parent on spVariant(parent)'

# EXTEND pfamXref TO COVER VARIANT SPLICE PROTEINS

hgsql proteins101005 -N -e \
'select pfamAC, variant, variant from spVariant, pfamXref where swissAC = parent and variant like "%-%" and swissAC=parent;' \
>pfamXrefVar.tab

hgLoadSqlTab -append proteins101005 pfamXref $kent/src/hg/lib/pfamXref.sql ./pfamXrefVar.tab

# move this endif statement past business that has successfully been completed
endif # BRACKET		


# SWITCH SYMBOLIC PROTEIN DATABASE LINKS (TBD)

# Ask system admin to switch the following symbolic database links:

       swissProt --> sp101005
       proteins  --> proteins101005

# Run some simple test on hgTracks, hgNear, hgGene, pbTracks, and pbGlobal  
# to make sure things are running OK.

# First check to see if pbGateway and pbGlobal are working.

# Then edit pbStamp.tab to adjust maximum y values for various stamps 
# and load it to pbStamp tables until all their scales look reasonable.
# For this particular release, no adjustment seems necessary.	

# move this exit statement to the end of the section to be done next
exit $status # BRACKET
    
#########################################################
# CREATE REACTOME TABLES 

# Obtain the ucsc_events24.dat.txt and ucsc_entity24.dat from Reactome.
# Contact: Gopinathrao, Gopal [gopinath@cshl.edu]
# Note - Gopal is no longer with Reactome, and the format has changed.  For now
# just using previous data.  Should double-check that Reactome links still work
# both on hg18 and with the hg19 build....

cd /hive/data/outside/reactome/reactome24

hgsql proteins101005 < $kent/src/hg/lib/spReactomeEvent.sql
hgsql proteins101005 -e 'load data local infile "ucsc_events24.tab" into table spReactomeEvent'

hgsql proteins101005 < $kent/src/hg/lib/spReactomeId.sql
hgsql proteins101005 -e 'load data local infile "ucsc_entity24.tab" into table spReactomeId'

# move this endif statement past business that has been successfully completed

#########################################################
# UPDATE REACTOME TABLES WITH V32 DATA (DONE, Fan 3/19/10)

# Obtain the ucsc_events32.dat.txt and ucsc_entity32.dat from Reactome.
# Contact: Lisa Matthews [lmatthews.nyumc@gmail.com]

ssh hgwdev
mkdir /hive/data/outside/reactome/reactome32
rm /hive/data/outside/reactome/current
ln -s /hive/data/outside/reactome/reactome32 /hive/data/outside/reactome/current
rm /hive/data/outside/reactome/reactome
ln -s /hive/data/outside/reactome/reactome32 /hive/data/outside/reactome/reactome 
cd /hive/data/outside/reactome/reactome

# save these two .dat files to this subdirectory.

cp ucsc_events32.dat ucsc_events32.tab
cp ucsc_entity32.dat ucsc_entity32.tab

# edit two .tab files to get rid of top head lines.

hgsql proteome -e 'drop table spReactomeEvent'
hgsql proteome < $kent/hg/lib/spReactomeEvent.sql
hgsql proteome -e 'load data local infile "ucsc_events32.tab" into table spReactomeEvent'

hgsql proteome -e 'drop table spReactomeId'
hgsql proteome < $kent/hg/lib/spReactomeId.sql
hgsql proteome -e 'load data local infile "ucsc_entity32.tab" into table spReactomeId'

# Generate lists for Reactome to link back to UCSC site.

hgsql hg17 -N -e 'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' |sort -u >hg17.lis

hgsql hg18 -N -e 'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' |sort -u >hg18.lis

hgsql hg19 -N -e 'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' |sort -u >hg19.lis

hgsql mm9 -N -e 'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' |sort -u >mm9.lis

hgsql mm8 -N -e 'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' |sort -u >mm8.lis

hgsql rn4 -N -e 'select kgId, kgXref.spId from kgXref,proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' |sort -u >rn4.lis

# !!! NOTE: Email the above 6 list files to Lisa Matthews [lmatthews.nyumc@gmail.com]
# AFTER THE NEW PROTEIN DBs ARE RELEASED ON RR.

#########################################################
# UPDATE REACTOME TABLES WITH V33 DATA (DONE, Fan 6/22/10)

# Obtain the ucsc_events33.dat.txt and ucsc_entity33.dat from Reactome.
# Contact: Robin Haw [Robin.Haw@oicr.on.ca]

ssh hgwdev
mkdir /hive/data/outside/reactome/reactome33
rm /hive/data/outside/reactome/current
ln -s /hive/data/outside/reactome/reactome33 /hive/data/outside/reactome/current
rm /hive/data/outside/reactome/reactome
ln -s /hive/data/outside/reactome/reactome33 /hive/data/outside/reactome/reactome 
cd /hive/data/outside/reactome/reactome

# save these two .dat files to this subdirectory.

cp ucsc_events33.dat ucsc_events33.tab
cp ucsc_entity33.dat ucsc_entity33.tab

# edit two .tab files to get rid of top head lines.

hgsql proteome -e 'drop table spReactomeEvent'
hgsql proteome < $kent/hg/lib/spReactomeEvent.sql
hgsql proteome -e 'load data local infile "ucsc_events33.tab" into table spReactomeEvent'

hgsql proteome -e 'drop table spReactomeId'
hgsql proteome < $kent/hg/lib/spReactomeId.sql
hgsql proteome -e 'load data local infile "ucsc_entity33.tab" into table spReactomeId'

# Generate lists for Reactome to link back to UCSC site.

hgsql hg17 -N -e 'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' |sort -u >hg17.lis

hgsql hg18 -N -e 'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' |sort -u >hg18.lis

hgsql hg19 -N -e 'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' |sort -u >hg19.lis

hgsql mm9 -N -e 'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' |sort -u >mm9.lis

hgsql mm8 -N -e 'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' |sort -u >mm8.lis

hgsql rn4 -N -e 'select kgId, kgXref.spId from kgXref,proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' |sort -u >rn4.lis

# !!! NOTE: Email the above 6 list files to Lisa Matthews [lmatthews.nyumc@gmail.com]
# AFTER THE NEW PROTEIN DBs ARE RELEASED ON RR.

#########################################################
# UPDATE REACTOME TABLES WITH V34 DATA (DONE, Fan 10/25/10)

# Obtain the ucsc_events34.dat.txt and ucsc_entity34.dat from Reactome.
# Contact: Robin Haw [Robin.Haw@oicr.on.ca]

ssh hgwdev
mkdir /hive/data/outside/reactome/reactome34
rm /hive/data/outside/reactome/current
ln -s /hive/data/outside/reactome/reactome34 /hive/data/outside/reactome/current
rm /hive/data/outside/reactome/reactome
ln -s /hive/data/outside/reactome/reactome34 /hive/data/outside/reactome/reactome 
cd /hive/data/outside/reactome/reactome

# save these two .dat files to this subdirectory.

cp ucsc_events34.dat ucsc_events34.tab
cp ucsc_entity34.dat ucsc_entity34.tab

# edit two .tab files to get rid of top head lines.

hgsql proteome -e 'drop table spReactomeEvent'
hgsql proteome < $kent/hg/lib/spReactomeEvent.sql
hgsql proteome -e 'load data local infile "ucsc_events34.tab" into table spReactomeEvent'

hgsql proteome -e 'drop table spReactomeId'
hgsql proteome < $kent/hg/lib/spReactomeId.sql
hgsql proteome -e 'load data local infile "ucsc_entity34.tab" into table spReactomeId'

# Generate lists for Reactome to link back to UCSC site.

hgsql hg17 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >hg17.lis

hgsql hg18 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >hg18.lis

hgsql hg19 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >hg19.lis

hgsql mm9 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >mm9.lis

hgsql mm8 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >mm8.lis

hgsql rn4 -N -e \
'select kgId, kgXref.spId from kgXref,proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >rn4.lis

# !!! NOTE: Email the above 6 list files to Lisa Matthews [lmatthews.nyumc@gmail.com]
# AFTER THE NEW PROTEIN DBs ARE RELEASED ON RR.

#########################################################
# UPDATE REACTOME TABLES WITH V35 DATA (DONE, Fan 01/03/10)

# Obtain the ucsc_events35 and ucsc_entity35 from Reactome.
# Contact: Robin Haw [Robin.Haw@oicr.on.ca]

ssh hgwdev
mkdir /hive/data/outside/reactome/reactome35
rm /hive/data/outside/reactome/current
ln -s /hive/data/outside/reactome/reactome35 /hive/data/outside/reactome/current
rm /hive/data/outside/reactome/reactome
ln -s /hive/data/outside/reactome/reactome35 /hive/data/outside/reactome/reactome 
cd /hive/data/outside/reactome/reactome

# save these two .dat files to this subdirectory.

cp ucsc_events35 ucsc_events35.tab
cp ucsc_entity35 ucsc_entity35.tab

# edit two .tab files to get rid of top head lines.

hgsql proteome -e 'drop table spReactomeEvent'
hgsql proteome < $kent/hg/lib/spReactomeEvent.sql
hgsql proteome -e 'load data local infile "ucsc_events35.tab" into table spReactomeEvent'

hgsql proteome -e 'drop table spReactomeId'
hgsql proteome < $kent/hg/lib/spReactomeId.sql
hgsql proteome -e 'load data local infile "ucsc_entity35.tab" into table spReactomeId'

# Generate lists for Reactome to link back to UCSC site.

hgsql hg17 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >hg17.lis

hgsql hg18 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >hg18.lis

hgsql hg19 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >hg19.lis

hgsql mm9 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >mm9.lis

hgsql mm8 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >mm8.lis

hgsql rn4 -N -e \
'select kgId, kgXref.spId from kgXref,proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >rn4.lis

# !!! NOTE: Email the above 6 list files to Lisa Matthews [lmatthews.nyumc@gmail.com]
# AFTER THE NEW PROTEIN DBs ARE RELEASED ON RR.

#########################################################
# UPDATE REACTOME TABLES WITH V36 DATA (DONE, Fan 03/18/2011)

# Obtain the ucsc_events36 and ucsc_entity36 from Reactome.
# Contact: Robin Haw [Robin.Haw@oicr.on.ca]

ssh hgwdev
mkdir /hive/data/outside/reactome/reactome36
rm /hive/data/outside/reactome/current
ln -s /hive/data/outside/reactome/reactome36 /hive/data/outside/reactome/current
rm /hive/data/outside/reactome/reactome
ln -s /hive/data/outside/reactome/reactome36 /hive/data/outside/reactome/reactome 
cd /hive/data/outside/reactome/reactome

# save these two .dat files to this subdirectory.

cp ucsc_events36.dat ucsc_events36.tab
cp ucsc_entity36.dat ucsc_entity36.tab

# edit two .tab files to get rid of top head lines.

hgsql proteome -e 'drop table spReactomeEvent'
hgsql proteome < $kent/hg/lib/spReactomeEvent.sql
hgsql proteome -e 'load data local infile "ucsc_events36.tab" into table spReactomeEvent'

hgsql proteome -e 'drop table spReactomeId'
hgsql proteome < $kent/hg/lib/spReactomeId.sql
hgsql proteome -e 'load data local infile "ucsc_entity36.tab" into table spReactomeId'

# Generate lists for Reactome to link back to UCSC site.

hgsql hg17 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >hg17.lis

hgsql hg18 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >hg18.lis

hgsql hg19 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >hg19.lis

hgsql mm9 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >mm9.lis

hgsql mm8 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >mm8.lis

hgsql rn4 -N -e \
'select kgId, kgXref.spId from kgXref,proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >rn4.lis

# !!! NOTE: Email the above 6 list files to Lisa Matthews [lmatthews.nyumc@gmail.com]
# AFTER THE NEW PROTEIN DBs ARE RELEASED ON RR.


#########################################################
# UPDATE REACTOME TABLES WITH V37 DATA (DONE, Fan 07/01/2011)

# Obtain the ucsc_events37 and ucsc_entity37 from Reactome.
# Contact: Robin Haw [Robin.Haw@oicr.on.ca]

ssh hgwdev
mkdir /hive/data/outside/reactome/reactome37
rm /hive/data/outside/reactome/current
ln -s /hive/data/outside/reactome/reactome37 /hive/data/outside/reactome/current
rm /hive/data/outside/reactome/reactome
ln -s /hive/data/outside/reactome/reactome37 /hive/data/outside/reactome/reactome 
cd /hive/data/outside/reactome/reactome

# save these two .dat files to this subdirectory.

cp ucsc_events37 ucsc_events37.tab
cp ucsc_entity37 ucsc_entity37.tab

# edit two .tab files to get rid of top head lines.

hgsql proteome -e 'drop table spReactomeEvent'
hgsql proteome < $kent/hg/lib/spReactomeEvent.sql
hgsql proteome -e 'load data local infile "ucsc_events37.tab" into table spReactomeEvent'

hgsql proteome -e 'drop table spReactomeId'
hgsql proteome < $kent/hg/lib/spReactomeId.sql
hgsql proteome -e 'load data local infile "ucsc_entity37.tab" into table spReactomeId'

# Generate lists for Reactome to link back to UCSC site.

hgsql hg17 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >hg17.lis

hgsql hg18 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >hg18.lis

hgsql hg19 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >hg19.lis

hgsql mm9 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >mm9.lis

hgsql mm8 -N -e \
'select kgId, kgXref.spId from kgXref, proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >mm8.lis

hgsql rn4 -N -e \
'select kgId, kgXref.spId from kgXref,proteome.spReactomeId,proteome.spVariant where kgXref.spID=proteome.spVariant.variant and spReactomeId.spId=parent' \
|sort -u >rn4.lis

# !!! NOTE: Email the above 6 list files to Lisa Matthews [lmatthews.nyumc@gmail.com]
# AFTER THE NEW PROTEIN DBs ARE RELEASED ON RR.

endif # BRACKET