942526536cf6261f16915b8c8c127829d70be133 hiram Tue Feb 22 13:14:24 2022 -0800 rework the content of the introduction text refs #28930 diff --git src/hg/gar/garTable.sh src/hg/gar/garTable.sh index 7bfeb76..2bbbafa 100755 --- src/hg/gar/garTable.sh +++ src/hg/gar/garTable.sh @@ -19,76 +19,72 @@ " # coordinate these colors with the table.pl definitions export criticalColor="#ff0000" export endangeredColor="#dd6600" export vulnerableColor="#663300" export leftHandPointer="☜" export rightHandPointer="☞" # printf "<a id='pageTop'></a>\n" printf "<h2>Genome assembly search and request</h2>\n" printf "<div id='canNotFindDiv' class='pullDownMenu'>\n" -printf " <span id='canNotFindAnchor'>after searching page,<br>cannot find desired assembly here</span'>\n" +printf " <span id='canNotFindAnchor'>Can't find your assembly ?</span'>\n" printf " <div class='pullDownMenuContent'>\n" -printf " <button id='specificRequest' type='button' onclick='gar.openModal(this)' name='specific'><label>%s request specific assembly not found here %s</label></button>\n", "${rightHandPointer}" "${leftHandPointer}" +printf " <button id='specificRequest' type='button' onclick='gar.openModal(this)' name='specific'><label>%s Press here to request an unlisted assembly %s</label></button>\n", "${rightHandPointer}" "${leftHandPointer}" printf " </div>\n" printf "</div>\n" -printf "<p>Please note discussion of <a href='http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#What' target=_blank>What does the Genome Browser do ?</a>\n" -printf "</p>\n" - -printf "<p>The information in this page allows navigation to -specific genome browsers when they are available. In the case where a -genome browser has not yet been constructed, the link for that species will -open a request form which will notify the U.C. Genome Browser staff as a request -to construct the genome browser for your species of interest. This is a new -and experimental service, we are interested to see if such requests are -many or few. Depending upon the level of activity, the expected processing -time for an assembly to appear in the genome browser should be on the order of -two weeks. +printf "<p>The UCSC Genome Browser provides a rapid and reliable display of any +requested portion of any genome assembly at any scale, together with dozens +of aligned annotation tracks (genes, mRNAs, CpG islands, regulation, +variation, repeats, and more). The Genome Browser stacks annotation tracks +beneath genome coordinate positions, allowing rapid visual correlation of +different types of information. The user can look at a whole chromosome to +get a feel for gene density, open a specific cytogenetic band to see a +positionally mapped disease gene candidate, or zoom in to a particular gene +to view its spliced ESTs and possible alternative splicing. The Genome Browser +itself does not draw conclusions; rather, it collates all relevant information +in one location, leaving the exploration and interpretation to the user. For +more information on using the UCSC Genome Browser please see our +<a href='https://genome.ucsc.edu/FAQ/' target=_blank>help</a> and +<a href='https://genome.ucsc.edu/training/index.html' target=_blank>training</a> +pages. +</p> +<p>This page lists both whole genome assembly browsers that are available for +immediate viewing, and assemblies that are not currently available but can +be requested. +</p> +<p>We are working on adding a search function to this page. Until then, please use the "find" feature of your Browser (commonly CTRL+F). +</p> +<p>After searching the page, if you do not find the assembly you are +interested in, you may request it using the "Request new assembly" +button at the top of the page. Complete the request form (including the +NCBI GenBank or RefSeq assembly accession identifier). You will be notified +by email when your assembly is available for viewing in the UCSC Genome +Browser. This can take up to three weeks. The assembly browser will include +the following annotation tracks: Assembly mapping, Base position, +Gaps (when present), GC Percent, Restriction Enzymes, Tandem Duplications, +CpG Islands, RefSeq mRNAs, Repeat Masking, and, if available: +NCBI RefSeq Genes and Ensembl Genes. +</p> +<p>This page is optimized for use in Firefox and Safari </p>\n" -printf "<p>Please note, not all possible assemblies are shown here. There is -nothing here from the clade categories: <em>archaea, viruses, bacteria</em>. -This display attempts to show only whole genome assemblies. Some assemblies -have been eliminated when their total assembly size is much smaller than the -typical genome size for such species. For example, only the <em>exome</em> -of the organism has been sequenced. And in some cases there are too many -assemblies for the same species, for example there are over 1,000 assemblies for <em>Homo sapiens</em>. -</p>\n" - -printf "<p>This page works best in the <em>Firefox</em> and <em>Safari</em> -web browsers. The web browsers <em>Chrome</em> and <em>Edge</em> take -almost a minute to prepare the page for use. -</p>\n" - -printf "<p>Use your web browser <em>find in page</em> function to search -for names of interest on this page. Make the entire set visiible to allow -the search to find everything. Future enhancements to this page may include -a better search system. -</p>\n" - -# printf "<p>The numbers in parenthesis following the -# <em>Scientific name (1,234)</em> indicate the number of assemblies available -# for that species. -# </p>\n" - -# my @clades = qw( primates mammals birds fish vertebrate invertebrates plants fungi ); cut -d' ' -f3,5 \ /cluster/home/hiram/kent/src/hg/makeDb/doc/asmHubs/master.run.list \ | sort | awk '{printf "%s\t%s\n", $1, $2};' > asmId.sciName sort -k1,1 -u \ /cluster/home/hiram/kent/src/hg/makeDb/doc/*AsmHub/*.orderList.tsv \ > asmId.commonName; sort -u /hive/data/outside/ncbi/genomes/reports/newAsm/*.suppressed.asmId.list \ > asmId.suppressed.list join -t$'\t' asmId.sciName asmId.commonName > asmId.sciName.commonName $srcDir/garTable.pl