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revision 1.12, Sun Jun 18 10:03:38 2006 UTC revision 1.17, Thu Jul 13 07:08:42 2006 UTC
# Line 112  Line 112 
112  } elsif (! -d $targetDir) {  } elsif (! -d $targetDir) {
113      Confess("Target directory $targetDir not found.");      Confess("Target directory $targetDir not found.");
114  } else {  } else {
115      # *Get the old Sprout.      # Get the old Sprout.
116      my $oldSprout = SFXlate->new_sprout_only($FIG_Config::oldSproutDB);      my $oldSprout = SFXlate->new_sprout_only($FIG_Config::oldSproutDB);
117      # Extract the genome group data from the old Sprout.      # Extract the genome group data from the old Sprout.
118      my %oldGroupHash = $oldSprout->GetGroups();      my %oldGroupHash = $oldSprout->GetGroups();
# Line 137  Line 137 
137              %oldGenomes = map { $_ => 1 } @{$oldGroupHash{$groupID}};              %oldGenomes = map { $_ => 1 } @{$oldGroupHash{$groupID}};
138          }          }
139          # Create the output file.          # Create the output file.
140          Open(\*GROUPFILE, ">$targetDir/$groupID.inc");          my $outFileName = "stats-" . lc($groupID) . ".inc";
141            Open(\*GROUPFILE, ">$targetDir/$outFileName");
142          # Get the styles.          # Get the styles.
143          my ($tableStyle, $markerStyle, @rowStyle) = ($options->{tableStyle}, $options->{markerStyle},          my ($tableStyle, $markerStyle, @rowStyle) = ($options->{tableStyle}, $options->{markerStyle},
144                                                       $options->{evenStyle}, $options->{oddStyle});                                                       $options->{evenStyle}, $options->{oddStyle});
# Line 177  Line 178 
178              # Get the number of PEGs.              # Get the number of PEGs.
179              my $pegCount = Tracer::CommaFormat($sprout->FeatureCount($genomeID, 'peg'));              my $pegCount = Tracer::CommaFormat($sprout->FeatureCount($genomeID, 'peg'));
180              # Get the number of RNAs.              # Get the number of RNAs.
181              my $rnaCount = Tracer::CommatFormat($sprout->FeatureCount($genomeID, 'rna'));              my $rnaCount = Tracer::CommaFormat($sprout->FeatureCount($genomeID, 'rna'));
182                # If there are no RNAs, we say we don't know the number, since we know there
183                # must be RNAs somewhere.
184                if (! $rnaCount) {
185                    $rnaCount = "n/d";
186                }
187              # Now we have four categories of features to work with, for each              # Now we have four categories of features to work with, for each
188              # combination of named or hypothetical vs. in-subsystem or              # combination of named or hypothetical vs. in-subsystem or
189              # not-in-subsystem. First, we get all of the feature assignments for              # not-in-subsystem. First, we get all of the feature assignments for

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