22a9ec8b34dd60a14257bdef408f21c03db601b4
hiram
  Mon Feb 17 16:06:38 2020 -0800
now using the shorter assembly name for genome identifier and fix some common names refs #23891

diff --git src/hg/makeDb/doc/asmHubs/mkSymLinks.pl src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
index a20691b..3564b72 100755
--- src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
+++ src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
@@ -1,102 +1,102 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 use File::Basename;
 
 my $argc = scalar(@ARGV);
 if ($argc != 2) {
   printf STDERR "mkSymLinks Name asmName\n";
   printf STDERR "e.g.: mkAsmStats Mammals mammals\n";
   exit 255;
 }
 my $Name = shift;
 my $asmHubName = shift;
 
 my %betterName;	# key is asmId, value is common name
 my $srcDocDir = "${asmHubName}AsmHub";
 
 my $home = $ENV{'HOME'};
 my $toolsDir = "$home/kent/src/hg/makeDb/doc/asmHubs";
 my $commonNameList = "$asmHubName.asmId.commonName.tsv";
 my $commonNameOrder = "$asmHubName.commonName.asmId.orderList.tsv";
 
 open (FH, "<$toolsDir/${commonNameList}") or die "can not read $toolsDir/${commonNameList}";
 while (my $line = <FH>) {
   next if ($line =~ m/^#/);
   chomp $line;
   my ($asmId, $name) = split('\t', $line);
   $betterName{$asmId} = $name;
 }
 close (FH);
 
 my @orderList;	# asmId of the assemblies in order from the *.list files
 # the order to read the different .list files:
 my $assemblyCount = 0;
 
 open (FH, "<$toolsDir/${commonNameOrder}") or die "can not read ${commonNameOrder}";
 while (my $line = <FH>) {
   next if ($line =~ m/^#/);
   chomp $line;
   my ($commonName, $asmId) = split('\t', $line);
   push @orderList, $asmId;
   ++$assemblyCount;
 }
 close (FH);
 
 my $destDir = "/hive/data/genomes/asmHubs";
 
 my $orderIndex = 0;
 foreach my $asmId (reverse(@orderList)) {
   ++$orderIndex;
   my ($gcPrefix, $accession, undef) = split('_', $asmId);
   my $accessionId = sprintf("%s_%s", $gcPrefix, $accession);
   printf STDERR "# %03d symlinks %s\n", $orderIndex, $accessionId;
   my $accessionDir = substr($asmId, 0 ,3);
   $accessionDir .= "/" . substr($asmId, 4 ,3);
   $accessionDir .= "/" . substr($asmId, 7 ,3);
   $accessionDir .= "/" . substr($asmId, 10 ,3);
 #  $accessionDir .= "/" . $asmId;
-  my $prevDestDir = "/hive/data/genomes/asmHubs/$accessionDir/$asmId";
+#  my $prevDestDir = "/hive/data/genomes/asmHubs/$accessionDir/$asmId";
   $destDir = "/hive/data/genomes/asmHubs/$accessionDir/$accessionId";
   my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir/$asmId";
 #  printf STDERR "# working '${buildDir}' '${destDir}'\n";
 #  printf STDERR "# working '${buildDir}' '${prevDestDir}'\n";
   if ( ! -d "${destDir}" ) {
     `mkdir -p "${destDir}"`;
   }
-  if ( -d "${prevDestDir}" ) {
-    printf STDERR "# rm -fr '${prevDestDir}'\n";
-    `rm -fr "${prevDestDir}"`;
-  }
+#  if ( -d "${prevDestDir}" ) {
+#    printf STDERR "# rm -fr '${prevDestDir}'\n";
+#    `rm -fr "${prevDestDir}"`;
+#  }
   `rm -f "${destDir}/bbi"`;
   `rm -f "${destDir}/ixIxx"`;
   `rm -fr "${destDir}/html"`;
   `mkdir -p "${destDir}/html"`;
   `rm -f "${destDir}/${accessionId}.2bit"`;
   `rm -f "${destDir}/${accessionId}.agp.gz"`;
   `rm -f "${destDir}/${accessionId}.chrom.sizes"`;
   `rm -f "${destDir}/${accessionId}_assembly_report.txt"`;
   `rm -f "${destDir}/trackDb.txt"`;
   `rm -f "${destDir}/genomes.txt"`;
   `rm -f "${destDir}/hub.txt"`;
   `rm -f "${destDir}/groups.txt"`;
   `ln -s "${buildDir}/bbi" "${destDir}/bbi"` if (-d "${buildDir}/bbi");
   `ln -s "${buildDir}/ixIxx" "${destDir}/ixIxx"` if (-d "${buildDir}/ixIxx");
   `ln -s ${buildDir}/html/*.html "${destDir}/html/"` if (-d "${buildDir}/html");
    my $jpgFiles =`ls ${buildDir}/html/*.jpg 2> /dev/null | wc -l`;
    chomp $jpgFiles;
    if ($jpgFiles > 0) {
     `rm -f ${destDir}/html/*.jpg`;
     `ln -s ${buildDir}/html/*.jpg "${destDir}/html/"`;
    }
 #  `ln -s ${buildDir}/html/*.png "${destDir}/genomes/${asmId}/html/"`;
   `ln -s "${buildDir}/${asmId}.2bit" "${destDir}/${accessionId}.2bit"` if (-s "${buildDir}/${asmId}.2bit");
   `ln -s "${buildDir}/${asmId}.agp.gz" "${destDir}/${accessionId}.agp.gz"` if (-s "${buildDir}/${asmId}.agp.gz");
   `ln -s "${buildDir}/${asmId}.chrom.sizes" "${destDir}/${accessionId}.chrom.sizes"` if (-s "${buildDir}/${asmId}.chrom.sizes");
   `ln -s "${buildDir}/download/${asmId}_assembly_report.txt" "${destDir}/${accessionId}_assembly_report.txt"` if (-s "${buildDir}/${asmId}_assembly_report.txt");
   `ln -s "${buildDir}/${asmId}.trackDb.txt" "${destDir}/trackDb.txt"` if (-s "${buildDir}/${asmId}.trackDb.txt");
   `ln -s "${buildDir}/${asmId}.genomes.txt" "${destDir}/genomes.txt"` if (-s "${buildDir}/${asmId}.genomes.txt");
   `ln -s "${buildDir}/${asmId}.hub.txt" "${destDir}/hub.txt"` if (-s "${buildDir}/${asmId}.hub.txt");
   `ln -s "${buildDir}/${asmId}.groups.txt" "${destDir}/groups.txt"` if (-s "${buildDir}/${asmId}.groups.txt");
 }