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revision 1.6, Fri Nov 5 21:07:52 2010 UTC revision 1.8, Wed Feb 2 15:43:10 2011 UTC
# Line 301  Line 301 
301          $stats->Add(orgDirGenomes => 1);          $stats->Add(orgDirGenomes => 1);
302          # We need to process all of this organism's TBL files.          # We need to process all of this organism's TBL files.
303          my $orgDirDir = "$FIG_Config::organisms/$orgDir/Features";          my $orgDirDir = "$FIG_Config::organisms/$orgDir/Features";
304            if (! -d $orgDirDir) {
305                Trace("No feature directory found for $orgDir.") if T(1);
306                $stats->Add(orgDirMissing => 1);
307            } else {
308          for my $ftype (OpenDir($orgDirDir, 1)) {          for my $ftype (OpenDir($orgDirDir, 1)) {
309              my $tblFileName = "$orgDirDir/$ftype/tbl";              my $tblFileName = "$orgDirDir/$ftype/tbl";
310              if (-s $tblFileName) {              if (-s $tblFileName) {
# Line 323  Line 327 
327                              $stats->Add(orgDirNormal => 1);                              $stats->Add(orgDirNormal => 1);
328                              # Yes. Write it normally.                              # Yes. Write it normally.
329                              WriteToMerge($mergeH, $alias, B => $aliasType, $fid);                              WriteToMerge($mergeH, $alias, B => $aliasType, $fid);
330                          } elsif ($alias =~ /^LocusTag:(.+)/ || $alias =~ /^locus\|(.+)/) {                              } elsif ($alias =~ /^LocusTag:(.+)/ || $alias =~ /^(?:locus|locus_tag|LocusTag)\|(.+)/) {
331                              # No, but this is a specially-marked locus tag.                              # No, but this is a specially-marked locus tag.
332                              $normalized = $1;                              $normalized = $1;
333                              $stats->Add(orgDirLocus => 1);                              $stats->Add(orgDirLocus => 1);
# Line 359  Line 363 
363              }              }
364          }          }
365      }      }
366        }
367      Trace("Organism directories complete.") if T(2);      Trace("Organism directories complete.") if T(2);
368  }  }
369    

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