src/utils/qa/makeUniProtFile.csh 1.2

Index: src/utils/qa/makeUniProtFile.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/makeUniProtFile.csh,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/utils/qa/makeUniProtFile.csh	14 May 2009 18:51:15 -0000	1.1
+++ src/utils/qa/makeUniProtFile.csh	14 May 2009 19:40:48 -0000	1.2
@@ -1,72 +1,77 @@
 #!/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 $db.rawDataForUniProt*
+# make the new directory and copy the file there
+mkdir -p /usr/local/apache/htdocs/goldenPath/$db/UCSCGenes
+cp $db.uniProtToUcscGenes.txt /usr/local/apache/htdocs/goldenPath/$db/UCSCGenes/uniProtToUcscGenes.txt
 
 # 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)"
+echo "Here's a sample of the $num line file you just created"
+echo " (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/$db.uniProtToUcscGenes.txt\n"
+echo " /usr/local/apache/htdocs/goldenPath/$db/UCSCGenes/uniProtToUcscGenes.txt"
+
+# clean up old files (except the real one)
+rm $db.rawDataForUniProt*
 
 exit 0