#!/bin/tcsh -efx

# uses the following binaries: pbHgnc spToSpXref2

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

set kent = ~/kent
set date = 121210
set spdate = 121210
set db = proteins$date
set spdb = sp$spdate

hgsqladmin create $db

cd /hive/data/inside/proteins
mkdir -p $date
cd $date
mkdir build

# Get HGNC data

wget -O hgnc.tab "http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=HGNC+output+data&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_locus_type&col=gd_locus_group&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_name_aliases&col=gd_pub_chrom_map&col=gd_date2app_or_res&col=gd_date_mod&col=gd_date_sym_change&col=gd_date_name_change&col=gd_pub_acc_ids&col=gd_enz_ids&col=gd_pub_eg_id&col=gd_pub_ensembl_id&col=gd_mgd_id&col=gd_other_ids&col=gd_other_ids_list&col=gd_pubmed_ids&col=gd_pub_refseq_ids&col=gd_gene_fam_name&col=gd_gene_fam_pagename&col=gd_record_type&col=gd_primary_ids&col=gd_secondary_ids&col=gd_ccds_ids&col=gd_vega_ids&col=gd_lsdb_links&col=md_gdb_id&col=md_eg_id&col=md_mim_id&col=md_refseq_id&col=md_prot_id&col=md_ensembl_id&col=md_ucsc_id&col=md_mgd_id&col=md_rgd_id&status=Approved&status=Entry+Withdrawn&status_opt=1&where=&order_by=gd_app_sym_sort&format=text&limit=&submit=submit&.cgifields=&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag"

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

#########################################################
# CREATE REACTOME TABLES 

# we're up to 42 now.  Got these from RM #7458
mkdir -p /hive/data/outside/reactome/reactome42
cd /hive/data/outside/reactome/reactome42

unzip reactome-ucsc_v42.zip
rm -rf __MACOSX/ reactome-ucsc_v42.zip
tail -n +7 ucsc_entity42 > ucsc_entity42.tab
tail -n +5 ucsc_events42 > ucsc_events42.tab

hgLoadSqlTab $db spReactomeEvent ~/kent/src/hg/lib/spReactomeEvent.sql ucsc_events42.tab
hgLoadSqlTab $db spReactomeId ~/kent/src/hg/lib/spReactomeId.sql ucsc_entity42.tab

cd ..
rm current reactome
ln -s /hive/data/outside/reactome/reactome42 current
ln -s /hive/data/outside/reactome/reactome42 reactome

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

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

# get records with HUGL symbol and descriptions
hgsql $spdb -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, $db.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 $spdb -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, $db.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 $spdb -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 $spdb -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 $spdb -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 $db spXref3 $kent/src/hg/lib/spXref3.sql spXref3.tab

# load the same data into a second temp table
hgLoadSqlTab $db 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 $db -e 'delete spXref3 from spXref3, spXref3B where spXref3.accession=spXref3B.accession and spXref3.hugoSymbol="" and spXref3B.hugoSymbol!=""'

# Drop temp table
hgsql $db -e "drop table spXref3B"

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

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

#stopped here
#	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 $db stdin pfamADesc.tab pfamAXref.tab >pfamXref.log

hgLoadSqlTab $db pfamDesc $kent/src/hg/lib/pfamDesc.sql pfamADesc.tab


hgLoadSqlTab $db 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/$date

hgsql $spdb -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 $db pdbSP $kent/src/hg/lib/pdbSP.sql pdbSP.tab

#	Build the spDisease table
cd /hive/data/inside/proteins/$date

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;' \
$spdb > spDisease.tab
wc  spDisease.tab
#   4909  289325 2100354 spDisease.tab

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

# create swInterPro table

cd /hive/data/inside/proteins/$date/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 position to match the old format
awk '{print $1,$4,$5,$6,$2,$3}' protein2ipr.dat > interProXref.tab

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

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

cd /hive/data/inside/proteins/$date
mkdir alias
cd alias

# this is very funky, but I'm leaving it in for the moment (braney)
hgsql $db -N -e 'select accession, accession,  "uAcc", "2006-01-15" from spXref3' >j1.tmp
hgsql $db -N -e 'select accession, accession2, "u2Ac", "2006-01-15" from spSecondaryID' >j2.tmp
hgsql $db -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

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

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

hgsql proteins111004 -N -e 'select * from spOldNew' >spOldNew.tab
hgLoadSqlTab $db spOldNew $kent/src/hg/lib/spOldNew.sql ./spOldNew.tab

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

# CREATE spVariant TABLE TO ENABLE UNIPROT VARIANT SPLICE ISOFORM PROCESSING 
cd /hive/data/inside/proteins/$date

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