147dce6b6804f24a5396a7ccb0b3bee184d1f6a7
hiram
Thu Jan 2 11:47:50 2020 -0800
set of files for hub build refs @24354
diff --git src/hg/makeDb/doc/globalReference/mkAsmStats.pl src/hg/makeDb/doc/globalReference/mkAsmStats.pl
new file mode 100755
index 0000000..8d0ce11
--- /dev/null
+++ src/hg/makeDb/doc/globalReference/mkAsmStats.pl
@@ -0,0 +1,270 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::stat;
+
+my $asmHubWorkDir = "globalReference";
+
+my @orderList; # asmId of the assemblies in order from the *.list files
+# the order to read the different .list files:
+my @classList = qw( human );
+my %class; # key is asmId, value is from class list
+my $assemblyCount = 0;
+my $overallNucleotides = 0;
+my $overallSeqCount = 0;
+my $overallGapSize = 0;
+my $overallGapCount = 0;
+
+my %ethnicGroup; # ksy is asmId, value is ethnicity
+my %countryOfOrigin; # ksy is asmId, value is country of origin
+
+##############################################################################
+# from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters:
+##############################################################################
+sub commify($) {
+ 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;
+
+print <<"END"
+
+
+
+
+
+
+Platinum Genomes Project assembly statistics
+
+This assembly hub contains assemblies released
+by the
+Platinum Genomes Project.
+
+
+
+
+
+
+Data resource links
+NOTE: Click on the column headers to sort the table by that column
+END
+}
+
+##############################################################################
+### start the table output
+##############################################################################
+sub startTable() {
+print <<"END"
+
+| count | ethnicity
link to genome browser |
+ country of origin
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);
+
+print <<"END"
+
+
+| TOTALS: | assembly count $assemblyCount |
+ $commaSeqCount |
+ $commaNuc |
+ $commaGapCount |
+ $commaGapSize |
+ |
+
|---|
+
+END
+}
+
+##############################################################################
+### end the HTML output
+##############################################################################
+sub endHtml() {
+print <<"END"
+
+
+
+
+