src/hg/utils/automation/featBitsSurvey.pl 819c30d6d5b5e898158949bb88d89026bd30bdf6

819c30d6d5b5e898158949bb88d89026bd30bdf6
hiram
  Fri May 3 15:53:04 2024 -0700
initial version of a feature bits table

diff --git src/hg/utils/automation/featBitsSurvey.pl src/hg/utils/automation/featBitsSurvey.pl
new file mode 100755
index 0000000..6156ab1
--- /dev/null
+++ src/hg/utils/automation/featBitsSurvey.pl
@@ -0,0 +1,84 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $argc = scalar(@ARGV);
+if ($argc < 1) {
+  printf STDERR "usage: featBitsSurvey.pl clade asmId [... asmId ...] > result.html\n";
+  exit 255;
+}
+
+printf '<!DOCTYPE HTML>
+<!--#set var="TITLE" value="Primates genomes assembly hubs" -->
+<!--#set var="ROOT" value="../.." -->
+
+<!--#include virtual="$ROOT/inc/gbPageStartHardcoded.html" -->
+';
+
+sub checkOne($) {
+  my ($fbTxt) = @_;
+  my $stat = "&nbsp;";
+  if ( -s "${fbTxt}" ) {
+    my $fBits = `cut -d' ' -f5 $fbTxt | tr -d '()%'`;
+    chomp $fBits;
+    $stat = $fBits;
+  } else {
+     printf STDERR "not found: '%s'\n", $fbTxt;
+  }
+  return $stat;
+}
+
+printf "<table class='sortable' border='1' style='background-color:powderblue;'>\n";
+printf "<caption>showing percent identity, how much of the target is matched by the query</caption>\n";
+printf "<thead style='position:sticky; top:0; background-color: white;'><tr>\n";
+printf "<th>count</th><th>chains</th><th>syntenic</th><th>reciprocal<br>best</th><th>lift<br>over</th><th>target</th><th>query</th><th>group</th>\n";
+printf "</tr></thead><tbody>\n";
+
+my $N = 0;
+my $clade = shift;
+while (my $asmId = shift) {
+  my @a = split('_', $asmId);
+  my $target = sprintf("%s_%s", $a[0], $a[1]);
+  my $gcX = substr($asmId, 0, 3);
+  my $d0 = substr($asmId, 4, 3);
+  my $d1 = substr($asmId, 7, 3);
+  my $d2 = substr($asmId, 10, 3);
+  my $tDir = "/hive/data/genomes/asmHubs/allBuild/$gcX/$d0/$d1/$d2/$asmId";
+  my $buildDir = `realpath "${tDir}"`;
+  chomp $buildDir;
+  if ( -d "${buildDir}" ) {
+    open ( my $td, "-|", "ls -d ${buildDir}/trackData/lastz.*") or die "can not ls -d ${buildDir}/trackData/lastz.*";
+    while (my $query = <$td>) {
+      chomp $query;
+      $query =~ s#.*/trackData/lastz.##;
+      my $Query = ucfirst($query);
+      my $fbTxt = "${buildDir}/trackData/lastz.${query}/fb.${target}.chain${Query}Link.txt";
+      my $fBits = checkOne($fbTxt);
+      $fbTxt = "${buildDir}/trackData/lastz.${query}/fb.${target}.chainSyn${Query}Link.txt";
+      my $synBits = checkOne($fbTxt);
+      $fbTxt = "${buildDir}/trackData/lastz.${query}/fb.${target}.chainRBest.${Query}.txt";
+      my $rbBits = checkOne($fbTxt);
+      $fbTxt = "${buildDir}/trackData/lastz.${query}/fb.${target}.chainLiftOver${Query}Link.txt";
+      my $loBits = checkOne($fbTxt);
+#      printf STDERR "%s\t%s\t%s\t%s\t%s\t%s\n", $target, $query, $fBits, $synBits, $rbBits, $loBits;
+      printf "<tr><td style='text-align:right;'>%4d</td>", ++$N;
+      printf "<td style='text-align:right;'>%s</td>", $fBits;;
+      printf "<td style='text-align:right;'>%s</td>", $synBits;
+      printf "<td style='text-align:right;'>%s</td>", $rbBits;
+      printf "<td style='text-align:right;'>%s</td>", $loBits;
+      printf "<td>%s</td><td>%s</td><td>%s</td></tr>\n", $target, $query, $clade;
+    }
+    close ($td);
+  } else {
+    printf STDERR "# %s - buildDir not found\n", $asmId;
+  }
+}
+printf "</tbody></table>\n";
+
+printf '</div><!-- closing gbsPage from gbPageStartHardcoded.html -->
+</div><!-- closing container-fluid from gbPageStartHardcoded.html -->
+<!--#include virtual="$ROOT/inc/gbFooterHardcoded.html"-->
+<script src="<!--#echo var="ROOT" -->/js/sorttable.js"></script>
+</body></html>
+';