89cf9d0784b0c1529f4a3638c3255f5b407be611 hiram Wed Jul 31 18:42:44 2019 -0700 add makefile to function from this source directory and cleaner html output via W3C validator checking refs #23734 diff --git src/hg/makeDb/doc/VGP/mkAsmStats.pl src/hg/makeDb/doc/VGP/mkAsmStats.pl index 9d5a381..65c01e7 100755 --- src/hg/makeDb/doc/VGP/mkAsmStats.pl +++ src/hg/makeDb/doc/VGP/mkAsmStats.pl @@ -1,72 +1,70 @@ #!/usr/bin/env perl use strict; use warnings; use File::stat; my @orderList; # asmId of the assemblies in order from the *.list files # the order to read the different .list files: -my @classList = qw( mammal bird amphibian fish ); +my @classList = qw( mammal bird reptile amphibian fish ); my %class; # key is asmId, value is from class list my $assemblyCount = 0; my $overallNucleotides = 0; my $overallSeqCount = 0; my $overallGapSize = 0; my $overallGapCount = 0; my %betterName; # key is asmId, value is common name ############################################################################## # from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters: ############################################################################## sub commify($) { 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" -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" - "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> -<!--#set var="TITLE" value="VGP - Vertebrate Genome Project assembly statistics - $timeStamp" --> +<!DOCTYPE HTML 4.01 Transitional> +<!--#set var="TITLE" value="VGP - Vertebrate Genomes Project assembly statistics - $timeStamp" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> -<h1>VGP - Vertebrate Genome Project assembly statistics - $timeStamp</h1> +<h1>VGP - Vertebrate Genomes Project assembly statistics - $timeStamp</h1> <p> This assembly hub contains some of the first complete assemblies released by the <a href='https://vertebrategenomesproject.org/' target=_blank> -<br><img src='VGPlogo.png' width=280 alt='VGP logo'><br> -Vertebrate Genome Project.</a> +Vertebrate Genomes Project.</a><br> +<img src='VGPlogo.png' width=280 alt='VGP logo'> </p> -<h3>See also: <a href='hubIndex.html' target=_blank>hub access</a> information</h3> - <p> -NOTE: <em>Click on the column headers to sort the table by that column</em> +<h3>See also: <a href='hubIndex.html' target=_blank>hub access</a> information</h3> </p> + <h3>Data resource links</h3> +NOTE: <em>Click on the column headers to sort the table by that column</em> END } ############################################################################## ### start the table output ############################################################################## sub startTable() { print <<"END" <table class="sortable" border="1"> <thead><tr><th>count</th><th>common name<br>view in browser</th> <th>scientific name</th> <th>NCBI assembly</th> <th>sequence<br>count</th><th>genome size<br>nucleotides</th> <th>gap<br>count</th><th>unknown bases<br>(gap size sum)</th><th>masking<br>percent</th> </tr></thead><tbody> @@ -90,40 +88,41 @@ <td align=right>$commaSeqCount</td> <td align=right>$commaNuc</td> <td align=right>$commaGapCount</td> <td align=right>$commaGapSize</td> <td colspan=1> </td> </tr></tfoot> </table> END } ############################################################################## ### end the HTML output ############################################################################## sub endHtml() { print <<"END" +</div><!-- closing gbsPage from gbPageStartHardcoded.html --> +</div><!-- closing container-fluid from gbPageStartHardcoded.html --> <!--#include virtual="\$ROOT/inc/gbFooterHardcoded.html"--> <script type="text/javascript" src="/js/sorttable.js"></script> </body></html> END } sub asmCounts($) { my ($chromSizes) = @_; my ($sequenceCount, $totalSize) = split('\s+', `ave -col=2 $chromSizes | egrep "^count|^total" | awk '{printf "%d\\n", \$NF}' | xargs echo`); - printf STDERR "# DBG: asmCounts: $sequenceCount, $totalSize\n"; return ($sequenceCount, $totalSize); } # my ($gapSize) = maskStats($faSizeTxt); sub maskStats($) { my ($faSizeFile) = @_; my $gapSize = `grep 'sequences in 1 file' $faSizeFile | awk '{print \$3}'`; chomp $gapSize; $gapSize =~ s/\(//; my $totalBases = `grep 'sequences in 1 file' $faSizeFile | awk '{print \$1}'`; chomp $totalBases; my $maskedBases = `grep 'sequences in 1 file' $faSizeFile | awk '{print \$9}'`; chomp $maskedBases; my $maskPerCent = 100.0 * $maskedBases / $totalBases; return ($gapSize, $maskPerCent); @@ -206,59 +205,59 @@ $commonName =~ s/.*\(//; $commonName =~ s/\)//; $sciName =~ s/.*:\s+//; $sciName =~ s/\s+\(.*//; } } elsif ($line =~ m/Taxid:/) { if ($taxId =~ m/notFound/) { ++$itemsFound; $taxId = $line; $taxId =~ s/.*:\s+//; } } } close (FH); $commonName = $betterName{$asmId} if (exists($betterName{$asmId})); - printf "<tr><th>%d</th><td align=center><a href='https://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/VGP/hub.txt&genome=%s&position=lastDbPos' target=_blank>%s</a></td>\n", ++$asmCount, $asmId, $commonName; + printf "<tr><th>%d</th><td align=center><a href='https://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/VGP/hub.txt&genome=%s&position=lastDbPos' target=_blank>%s</a></td>\n", ++$asmCount, $asmId, $commonName; printf " <td align=center>%s</td>\n", $sciName; printf " <td align=left><a href='https://www.ncbi.nlm.nih.gov/assembly/%s_%s/' target=_blank>%s</a></td>\n", $gcPrefix, $asmAcc, $asmId; printf " <td align=right>%s</td>\n", commify($seqCount); printf " <td align=right>%s</td>\n", commify($totalSize); printf " <td align=right>%s</td>\n", commify($gapCount); printf " <td align=right>%s</td>\n", commify($gapSize); printf " <td align=right>%.2f</td>\n", $maskPerCent; printf "</tr>\n"; } } ############################################################################## ### main() ############################################################################## +my $home = $ENV{'HOME'}; +my $srcDir = "$home/kent/src/hg/makeDb/doc/VGP"; -open (FH, "<commonNames.txt") or die "can not read commonNames.txt"; +open (FH, "<$srcDir/commonNames.txt") or die "can not read $srcDir/commonNames.txt"; while (my $line = <FH>) { chomp $line; my ($asmId, $name) = split('\t', $line); $betterName{$asmId} = $name; } close (FH); - foreach my $species (@classList) { - my $listFile = "${species}.list"; - printf STDERR "%s\n", $listFile; + my $listFile = "$srcDir/${species}.list"; open (FH, "<$listFile") or die "can not read $listFile"; while (my $asmId = <FH>) { chomp $asmId; push @orderList, $asmId; $class{$asmId} = $species; ++$assemblyCount; } close (FH); } startHtml(); startTable(); tableContents(); endTable(); endHtml();