5cd7aa7b3364cb744c638c16fd0ca95015dd6079
braney
  Thu Apr 25 09:57:53 2024 -0700
small change to allow script to recognize knownGeneV<number><anyText> as
a mammal.

diff --git src/hg/utils/automation/doHgNearBlastp.pl src/hg/utils/automation/doHgNearBlastp.pl
index c87c626..21f5f74 100755
--- src/hg/utils/automation/doHgNearBlastp.pl
+++ src/hg/utils/automation/doHgNearBlastp.pl
@@ -296,33 +296,33 @@
 # 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;
 
 sub calcE {
   # Look up the blastp e parameter (max E-value) by clade distances
   my ($tDb, $qDb) = @_;
-  (my $t = $tDb) =~ s/\d+$//;
+  (my $t = $tDb) =~ s/\d+.*$//;
   defined ($t = $dbToClade{$t}) || die "Can't figure out clade of '$tDb'";
-  (my $q = $qDb) =~ s/\d+$//;
+  (my $q = $qDb) =~ s/\d+.*$//;
   defined ($q = $dbToClade{$q}) || die "Can't figure out clade of '$qDb'";
   my $e = $cladeEs[$t][$q] || die "No e for clades '$t', '$q'";
   return $e;
 } # calcE
 
 sub runPairwiseBlastp {
   # Do a pairwise blastp cluster run for the given query.  
   # $b is the blastp -b param value... note -b is at the end of $blastpParams.
   my ($tDb, $qDb, $e, $b) = @_;
 
   my $runDir = "$buildDir/run.$tDb.$qDb";
   &HgAutomate::mustMkdir($runDir);
   my $fh = &HgAutomate::mustOpen(">$runDir/blastSome");
   print $fh <<_EOF_
 #!/bin/csh -ef