b99d9ad5adfa3176196acb5f4ace0c98f9742646
hiram
Fri May 22 14:13:48 2020 -0700
eliminate other hub indexes for VGP page index refs #25555
diff --git src/hg/makeDb/doc/asmHubs/mkAsmStats.pl src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
index eaafb3c..85afdfa 100755
--- src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
+++ src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
@@ -1,362 +1,377 @@
#!/usr/bin/env perl
use strict;
use warnings;
use File::stat;
my $argc = scalar(@ARGV);
if ($argc != 2) {
printf STDERR "mkAsmStats Name asmName\n";
printf STDERR "e.g.: mkAsmStats Mammals mammals\n";
exit 255;
}
my $Name = shift;
my $asmHubName = shift;
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";
my @orderList; # asmId of the assemblies in order from the *.list files
# the order to read the different .list files:
my %betterName; # key is asmId, value is better common name than found in
# assembly_report
my $vgpIndex = 0;
$vgpIndex = 1 if ($Name =~ m/vgp/i);
my $assemblyTotal = 0; # complete list of assemblies in this group
my $asmCount = 0; # count of assemblies completed and in the table
my $overallNucleotides = 0;
my $overallSeqCount = 0;
my $overallGapSize = 0;
my $overallGapCount = 0;
##############################################################################
# from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters:
##############################################################################
sub commify($) {
my $text = reverse $_[0];
$text =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g;
return scalar reverse $text
}
##############################################################################
### start the HTML output
##############################################################################
sub startHtml() {
my $timeStamp = `date "+%F"`;
chomp $timeStamp;
my $subSetMessage = "subset of $asmHubName only";
if ($asmHubName eq "vertebrate") {
$subSetMessage = "subset of other ${asmHubName}s only";
}
if ($vgpIndex) {
print <<"END"
VGP - Vertebrate Genomes Project assembly hubs, assembly statistics
This assembly hub contains assemblies released
by the
Vertebrate Genomes Project.
END
} else {
print <<"END"
$Name Genomes assembly hubs, assembly statistics
Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage.
END
}
print <<"END"
Data resource links
NOTE: Click on the column headers to sort the table by that column
The link to genome browser will attach only that single assembly to
the genome browser.
END
}
##############################################################################
### start the table output
##############################################################################
sub startTable() {
print <<"END"
| count |
common name
link to genome browser |
scientific name
and data download |
NCBI assembly |
sequence
count | genome size
nucleotides |
gap
count | unknown bases
(gap size sum) | masking
percent |
|---|
END
}
##############################################################################
### end the table output
##############################################################################
sub endTable() {
my $commaNuc = commify($overallNucleotides);
my $commaSeqCount = commify($overallSeqCount);
my $commaGapSize = commify($overallGapSize);
my $commaGapCount = commify($overallGapCount);
my $percentDone = 100.0 * $asmCount / $assemblyTotal;
my $doneMsg = "";
if ($asmCount < $assemblyTotal) {
$doneMsg = sprintf(" (%d build completed, %.2f %% finished)", $asmCount, $percentDone);
}
if ($assemblyTotal > 1) {
- print <<"END"
-
+ print "
| TOTALS: | total assembly count ${assemblyTotal}${doneMsg} |
$commaSeqCount |
$commaNuc |
$commaGapCount |
$commaGapSize |
|
-
|---|
+
+";
+
+ # try extra column headers as last row for this very large index page
+ if ($vgpIndex) {
+ print "| count |
+ common name
link to genome browser |
+ scientific name
and data download |
+ NCBI assembly |
+ sequence
count | genome size
nucleotides |
+ gap
count | unknown bases
(gap size sum) | masking
percent |
+
|---|
+";
+ }
+
+ print "
+
-END
-} else {
- print <<"END"
+";
+ } else {
+ print "
-END
-}
+";
+ } # $assemblyTotal <= 1
} # sub endTable()
##############################################################################
### end the HTML output
##############################################################################
sub endHtml() {
# do not print these links for VGP index
if ((0 == $vgpIndex) && ($asmHubName ne "viral")) {
printf "\n
\n\n";
}
print <<"END"