#!/bin/tcsh -efx
# Script to create a relational version of UniProt database.  Should be run on
# hgwdev.

set DBDATE=150225
set DB=sp$DBDATE

# Set up working directory
mkdir -p /hive/data/outside/uniProt/$DBDATE/build

# Download uniProt. This will take about 12 hours
cd /hive/data/outside/uniProt/$DBDATE/build
wget ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
#  523,470,864 16.0M/s   in 41s  
wget ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.dat.gz
# 50,308,178,357 12.4M/s   in 67m 44s
wget ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot_varsplic.fasta.gz
#  7,860,658   1.95M/s   in 4.2s

# Turn flat file into relational tab-separated files.
# strip out evidence tags
zcat *.dat.gz | /cluster/home/braney/bin/x86_64/stripEvidence stdin stdout |  /cluster/home/braney/bin/x86_64/spToDb stdin ../tabFiles

cd ../tabFiles
wc -l *.txt | awk '{print $2,$1}' | sort > counts
cd ../..
join 140122/tabFiles/counts 150225/tabFiles/counts | awk '{print $1, $3/$2}' | awk '{if (($2 > 2) || ($2 < 0.5)) print}'

# accToKeyword.txt 2.17571
# accToTaxon.txt 3.43881
# commonName.txt 0.136933
# taxon.txt 0.0283836

# Create the database.  
hgsql mm10 -e "create database sp$DBDATE"

# Load it up with table definitions from source directory
hgsql sp$DBDATE < ~/kent/src/hg/protein/spToDb/spDb.sql

# Load up the data from tab files.  This takes about an hour.
set s=`date +%s`
cd /hive/data/outside/uniProt/$DBDATE/tabFiles
foreach i (*.txt)
  hgsqlimport --local sp$DBDATE $i
end
set e=`date +%s`
expr $e - $s

# 23604


# Add varsplice info 
zcat ../build/uniprot_sprot_varsplic.fasta.gz | spDbAddVarSplice sp$DBDATE stdin .
hgLoadSqlTab sp$DBDATE -notOnServer -append varProtein /dev/null varProtein.txt
hgLoadSqlTab sp$DBDATE -notOnServer -append protein /dev/null varProtein.txt
hgLoadSqlTab sp$DBDATE -notOnServer -append varAcc /dev/null varAcc.txt
hgLoadSqlTab sp$DBDATE -notOnServer -append displayId /dev/null varDisplayId.txt
hgLoadSqlTab sp$DBDATE -notOnServer -append accToTaxon /dev/null varAccToTaxon.txt
hgLoadSqlTab sp$DBDATE -notOnServer -append geneLogic /dev/null varGeneLogic.txt
hgLoadSqlTab sp$DBDATE -notOnServer -append gene /dev/null varGene.txt
hgLoadSqlTab sp$DBDATE -notOnServer -append description /dev/null varDescription.txt

# Add table descriptions
makeTableDescriptions sp$DBDATE ~/kent/src/hg/protein/spToDb/spDbTables.as

# Zip up tab files for people who prefer them to database.
gzip *.txt