d0aad7f66c2fee0fa9366c3b3caf4d761750c055
braney
  Tue Aug 17 10:27:07 2021 -0700
first version of Gencode genes (knownGene version) for mm39

diff --git src/hg/utils/automation/doHgNearBlastp.pl src/hg/utils/automation/doHgNearBlastp.pl
index 3234c87..c87c626 100755
--- src/hg/utils/automation/doHgNearBlastp.pl
+++ src/hg/utils/automation/doHgNearBlastp.pl
@@ -276,31 +276,31 @@
 $blastPath/bin/formatdb -i $qFasta -t $qDb -n $qDb
 _EOF_
     ;
   close($fh);
   &HgAutomate::run("chmod a+x $bossScript");
   &HgAutomate::nfsNoodge("$bossScript");
   &HgAutomate::run("$HgAutomate::runSSH $distrHost nice $bossScript");
 } # formatSequence
 
 # Make a matrix of clade-pair -e (max E-value) threshold:
 my ($mammal, $fish, $fly, $worm, $yeast) = (0..5);
 my %dbToClade = ( hg => $mammal, mm => $mammal, rn => $mammal, tmpFoo => $mammal,
 		  danRer => $fish,
 		  dm => $fly,
 		  ce => $worm,
-		  sacCer => $yeast, );
+		  sacCer => $yeast, knownGeneV => $mammal, knownGeneVM => $mammal, );
 my @cladeEs;
 # Different species within clade (not self alignments -- see $selfE):
 $cladeEs[$mammal][$mammal] = $cladeEs[$fish][$fish] = $cladeEs[$fly][$fly] =
     $cladeEs[$worm][$worm] = $cladeEs[$yeast][$yeast] = 0.001;
 # Cross-clade:
 $cladeEs[$mammal][$fish]  = $cladeEs[$fish][$mammal]  = 0.005;
 $cladeEs[$mammal][$fly]   = $cladeEs[$fly][$mammal]   = 0.01;
 $cladeEs[$mammal][$worm]  = $cladeEs[$worm][$mammal]  = 0.01;
 $cladeEs[$mammal][$yeast] = $cladeEs[$yeast][$mammal] = 0.01;
 $cladeEs[$fish][$fly]   = $cladeEs[$fly][$fish]   = 0.01;
 $cladeEs[$fish][$worm]  = $cladeEs[$worm][$fish]  = 0.01;
 $cladeEs[$fish][$yeast] = $cladeEs[$yeast][$fish] = 0.01;
 $cladeEs[$fly][$worm]  = $cladeEs[$worm][$fly]  = 0.01;
 $cladeEs[$fly][$yeast] = $cladeEs[$yeast][$fly] = 0.01;
 $cladeEs[$worm][$yeast] = $cladeEs[$yeast][$worm] = 0.01;
@@ -361,31 +361,32 @@
   &HgAutomate::nfsNoodge("$bossScript");
   &HgAutomate::run("$HgAutomate::runSSH $clusterHub $bossScript");
 } # runPairwiseBlastp
 
 
 sub dbToPrefix {
   # Condense database name to a 2-character prefix for the *BlastTab table.
   my ($db) = @_;
   my $prefix;
   return $targetAbbrev if ($targetAbbrev && $db eq $tDb);
   if ($db =~ /^(\w\w)\d+$/) {
     $prefix = $1;
   } elsif ($db =~ /^(\w)\w\w(\w)\w\w\d+$/) {
     $prefix = $1 . lc($2);
   } else {
-    die "Error: dbToPrefix: expecting database name, got $db";
+    # just use the whole db name
+    $prefix = $db;
   }
   return $prefix;
 }
 
 sub loadPairwise {
   my ($tDb, $qDb, $tablePrefix, $max, $filePattern) = @_;
 
   $filePattern = 'out/*.tab' if (! defined $filePattern);
   my $tableName = $tablePrefix . 'BlastTab';
   my $bestOnly = ($max > 1) ? '-bestOnly' : '';
   my $runDir = "$buildDir/run.$tDb.$qDb";
   my $bossScript = "$buildDir/run.$tDb.$qDb/loadPairwise.csh";
   my $fh = HgAutomate::mustOpen(">$bossScript");
   print $fh <<_EOF_
 #!/bin/csh -efx