src/utils/qa/makeUniProtFile.csh 1.1

Index: src/utils/qa/makeUniProtFile.csh
===================================================================
RCS file: src/utils/qa/makeUniProtFile.csh
diff -N src/utils/qa/makeUniProtFile.csh
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/utils/qa/makeUniProtFile.csh	14 May 2009 18:51:15 -0000	1.1
@@ -0,0 +1,72 @@
+#!/bin/tcsh
+source `which qaConfig.csh`
+
+########################################
+# 
+# Ann Zweig 5-2009
+#
+# Use this script to create a file for the folks at UnitProt.
+# They will use the file to create links from their web site back to our
+# UCSC Gene details pages.
+#
+########################################
+
+set db=''
+set org=''
+set hasKGs=''
+set num=''
+
+if ($#argv != 1 ) then
+ echo
+ echo " Use this script to create a mapping of UniProt IDs to UCSC Gene ID."
+ echo " UniProt will pick it up from our download server and use it to"
+ echo " create links from their web site to our gene details pages."
+ echo
+ echo "    usage: db"
+ echo
+ exit 1
+else
+ set db=$argv[1]
+endif
+
+# run only from hgwdev
+if ( "$HOST" != "hgwdev" ) then
+ echo "\nERROR: you must run this script on hgwdev!\n"
+ exit 1
+endif
+
+# make sure this assembly has UCSC Genes
+set hasKGs=`hgsql -Ne "SELECT genomeDb FROM gdbPdb" hgcentraltest | grep "$db"`
+if ( '' == $hasKGs ) then
+ echo " \nERROR: this assembly does not appear to have a UCSC Genes track\n"
+ exit 1
+endif
+
+# get the data from the two tables
+hgsql -Ne "SELECT displayId, kgId FROM kgProtAlias" $db > $db.rawDataForUniProt
+hgsql -Ne "SELECT spId, kgId FROM kgSpAlias WHERE spId != ''" $db >> $db.rawDataForUniProt
+
+# make sure there is only one UCSC Gene ID - UniProt ID pair
+sort -k1,1 -u $db.rawDataForUniProt > $db.rawDataForUniProt.sorted
+
+# find out the name of the organism for this database
+set org=`hgsql -Ne 'SELECT organism FROM dbDb where name = "'$db'" LIMIT 1' hgcentraltest\
+ | perl -wpe '$_ = lcfirst($_)'`
+
+# now add the organism name to every row
+cat $db.rawDataForUniProt.sorted | sed -e 's/$/ '"$org"'/g' > $db.uniProtToUcscGenes.txt
+
+# clean up old files
+rm $db.rawDataForUniProt*
+
+# how big is the file
+set num=`cat $db.uniProtToUcscGenes.txt | wc -l`
+
+# explain the output to the user
+echo "\nSUCCESS!\n"
+echo "Here's a sample of the $num line file you just created (expect: UniProtId ucscGeneId orgName)"
+head $db.uniProtToUcscGenes.txt
+echo " \nAsk for a push of your new file to hgdownload:\n"
+echo " /usr/local/apache/htdocs/goldenPath/$db/UCSCGenes/$db.uniProtToUcscGenes.txt\n"
+
+exit 0