1b98e807b0cd136bb8df9d914a531781bcfa3ea3
pauline
  Tue Mar 20 18:29:35 2012 -0700
Fixed a typo I should have caught in code review redmine 7287
diff --git src/utils/qa/makeUniProtFile.csh src/utils/qa/makeUniProtFile.csh
index ceb399b..d9d53f7 100755
--- src/utils/qa/makeUniProtFile.csh
+++ src/utils/qa/makeUniProtFile.csh
@@ -1,116 +1,116 @@
 #!/bin/tcsh
 source `which qaConfig.csh`
 
 ########################################
 # 
 # Ann Zweig 05-2009
 #
 # 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
 # Gene details pages.
 #
 ########################################
 
 onintr cleanup
 
 set db=''
 set org=''
 set hasKGs=''
 set num=''
 
 if ($#argv != 1 ) then
  echo
  echo "  Use this script to create a mapping of UniProt IDs to Gene IDs. \
   UniProt will pick it up from our download server and use it to \
   create links from their web site to our gene details pages. For the \
   gene sets from outside sources, check this script first to be sure it is \
   using the most up-to-date tables."
  echo
  echo "    usage: db"
  echo
  exit 1
 else
  set db=$argv[1]
 endif
 
 # run only from hgwdev
 if ( "$HOST" != "hgwdev" ) then
  echo "\nERROR: you must run this script on hgwdev!\n"
  exit 1
 endif
 
 # human and mouse use an official UCSC Genes build
 if ( $db =~ "hg*" || $db =~ "mm*" ) then
  # get the data from the two KG-related tables
  hgsql -Ne "SELECT displayId, kgId FROM kgProtAlias" \
   $db > $db.rawDataForUniProt
  hgsql -Ne "SELECT spId, kgId FROM kgSpAlias WHERE spId != ''" \
   $db >> $db.rawDataForUniProt
 
 else #non-UCSC Gene assembly
  # each of the non-KG assemblies are treated a little differently
 
  if ( $db =~ "rn*" ) then
-  hgsql -Ne "hgsql -Ne "SELECT value, name FROM rgdGene2ToUniProt" $db > $db.rawDataForUniProt
+  hgsql -Ne "SELECT value, name FROM rgdGene2ToUniProt" $db > $db.rawDataForUniProt
  endif
 
  if ( $db =~ "dm*" ) then
   hgsql -Ne "SELECT alias, a.name FROM flyBase2004Xref AS a, \
    flyBaseToUniProt AS b WHERE a.name=b.name AND alias != 'n/a'" \
    $db > $db.rawDataForUniProt 
  endif
 
  if ( $db =~ "ce*" ) then
   hgsql -Ne "SELECT acc, name FROM sangerGene AS a, uniProt.gene AS b \
    WHERE a.proteinID=b.val and acc != 'n/a'" $db > $db.rawDataForUniProt
  endif
  
  if ( $db =~ "danRer*" ) then
   echo " \nERROR: Although a file could be generated for danRer, uniProt has"
   echo " decided that they do not want to do that mapping...yet\n" 
   exit 1
  endif
  
  if ( $db =~ "sacCer*" ) then
   echo " \nERROR: Although a file could be generated for sacCer, uniProt has"
   echo " decided that they do not want to do that mapping...yet\n" 
   exit 1
  endif
 endif
 
 if ( -e $db.rawDataForUniProt ) then 
  # find out the name of the organism for this database
  set org=`hgsql -Ne 'SELECT organism FROM dbDb where name = "'$db'" LIMIT 1' \
   hgcentraltest | perl -wpe '$_ = lcfirst($_)'`
 
  # now add the organism name to every row
  sed -e 's/$/ '$org'/' $db.rawDataForUniProt > $db.rawDataForUniProt.plus
 
 else
   echo " \nERROR: It is not possible to make a mapping file for UniProt from"
   echo " the database you entered: $db\n"
   exit 1
 endif
 
 # make sure there is only one Gene ID - UniProt ID pair
 sort -k1,1 -u $db.rawDataForUniProt.plus > $db.uniProtToUcscGenes.txt
 
 # make the new directory and copy the file there
 mkdir -p /usr/local/apache/htdocs-hgdownload/goldenPath/$db/UCSCGenes
 cp $db.uniProtToUcscGenes.txt /usr/local/apache/htdocs-hgdownload/goldenPath/$db/UCSCGenes/uniProtToUcscGenes.txt
 
 # how big is the file
 set num=`wc -l $db.uniProtToUcscGenes.txt | awk '{print $1}'`
 
 # explain the output to the user
 echo "\nSUCCESS!\n"
 echo "Here's a sample of the ${num}-line file you just created"
 echo " (expect: UniProtId ucscGeneId orgName)"
 head $db.uniProtToUcscGenes.txt
 echo " \nAsk for a push of your new file to hgdownload:\n"
 echo " /usr/local/apache/htdocs-hgdownload/goldenPath/$db/UCSCGenes/uniProtToUcscGenes.txt"
 # clean up old files (except the real one)
 cleanup:
 rm -f $db.rawDataForUniProt*
 
 exit 0