src/hg/utils/automation/doHgNearBlastp.pl 1.9

Index: src/hg/utils/automation/doHgNearBlastp.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/doHgNearBlastp.pl,v
retrieving revision 1.8
retrieving revision 1.9
diff -b -B -U 4 -r1.8 -r1.9
--- src/hg/utils/automation/doHgNearBlastp.pl	9 Jul 2009 22:21:24 -0000	1.8
+++ src/hg/utils/automation/doHgNearBlastp.pl	9 Jul 2009 23:17:51 -0000	1.9
@@ -276,9 +276,9 @@
   &HgAutomate::run("chmod a+x $bossScript");
   &HgAutomate::run("$HgAutomate::runSSH $distrHost nice $bossScript");
 } # formatSequence
 
-# Make a matrix of clade-pair -e (max error) values:
+# 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,
 		  danRer => $fish,
 		  dm => $fly,
@@ -300,9 +300,9 @@
 $cladeEs[$fly][$yeast] = $cladeEs[$yeast][$fly] = 0.01;
 $cladeEs[$yeast][$yeast] = $cladeEs[$yeast][$yeast] = 0.01;
 
 sub calcE {
-  # Look up the blastp e parameter (max error) by clade distances
+  # Look up the blastp e parameter (max E-value) by clade distances
   my ($tDb, $qDb) = @_;
   (my $t = $tDb) =~ s/\d+$//;
   defined ($t = $dbToClade{$t}) || die "Can't figure out clade of '$tDb'";
   (my $q = $qDb) =~ s/\d+$//;