f654134d5172e2687b3e6f98da7db78dd8379387
hiram
Tue Jan 21 15:01:57 2020 -0800
initial set of files to build "other vertebrates" assembly hub refs #2482
diff --git src/hg/makeDb/doc/vertebratesAsmHub/mkAsmStats.pl src/hg/makeDb/doc/vertebratesAsmHub/mkAsmStats.pl
new file mode 100755
index 0000000..1f255f3
--- /dev/null
+++ src/hg/makeDb/doc/vertebratesAsmHub/mkAsmStats.pl
@@ -0,0 +1,262 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::stat;
+
+my $home = $ENV{'HOME'};
+my $Name = "Vertebrate";
+my $asmHubName = "vertebrate";
+my $srcDocDir = "${asmHubName}sAsmHub";
+my $asmHubDocDir = "$home/kent/src/hg/makeDb/doc/$srcDocDir";
+
+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 $assemblyCount = 0;
+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 $timeStamp;
+
+print <<"END"
+
+
+
+
+
+
+$Name Genomes assembly hubs
+
+Assemblies from NCBI/Genbank/Refseq sources, subset of other $asmHubName only.
+
+
+
+
+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);
+
+print <<"END"
+
+
+| TOTALS: | assembly count $assemblyCount |
+ $commaSeqCount |
+ $commaNuc |
+ $commaGapCount |
+ $commaGapSize |
+ |
+
|---|
+
+END
+}
+
+##############################################################################
+### end the HTML output
+##############################################################################
+sub endHtml() {
+print <<"END"
+
+
+
+
+