1ff9db2c7a16fbc5f3ef80468cea9c0d93469b22 hiram Thu Feb 24 14:05:28 2022 -0800 add a column 1 tool tip to indicate request or browser refs #28930 diff --git src/hg/gar/garTable.pl src/hg/gar/garTable.pl index f4ee5ed..3592cfa 100755 --- src/hg/gar/garTable.pl +++ src/hg/gar/garTable.pl @@ -738,32 +738,32 @@ printf "
    • \n"; printf "
    • \n"; printf " \n"; printf " \n"; printf "\n"; printf "
    \n"; printf " show/hide columns\n"; printf "
    \n"; printf " \n"; printf "
    \n"; printf "
    \n\n"; printf " \n"; printf " \n\n"; printf "\n"; printf "\n"; printf "

    . . . please wait while page loads . . .

    \n\n"; @@ -786,42 +786,42 @@ printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; -printf "
    common nameThe common name links to a genome browser when it exists, or provides a request form to ask for the assembly to be added to the system
    \n"; -printf "
    scientific name (count)The numbers in parenthesis (1234) following the name indicates the number of assemblies available for this species. The link does a google image search for that name.
    \n"; -printf "
    NCBI assemblyThe NCBI assembly provides a link to the NCBI resource record for this assembly
    \n"; -printf "
    assembly
    sizeThe assembly size is the total number of nucleotides in the assembly.
    \n"; -printf "
    sequence
    countThe sequence count is the number of sequences in this assembly.
    \n"; -printf "
    scaffold N50
    size (L50)The scaffold N50 is the N50 measurement for this assembly.
    \n"; -printf "
    contig N50
    size (L50)The contig N50 is the N50 measurement for this assembly when there are contigs to measure.
    \n"; -printf "
    I
    U
    C
    NIUCN status column is the status from the IUCN (2021) Red List of Threatened species, Version 2021-3, accessed on 17 Dec 2021 CR - Critical / EN - Endangered / VU - Vulnerable The link goes to the IUCN web site for more information for that species.
    \n", $statusColors{"CR"}, $statusColors{"EN"}, $statusColors{"VU"}; -printf "
    NCBI taxIDThe taxID links to the NCBI taxonomy database.
    \n"; -printf "
    assembly
    dateThe submission date for this assembly to the NCBI assembly system.
    \n"; -printf "
    submitter of assemblyThe name of the organization that produced this assembly.
    \n"; -printf "
    cladeIndicating the clade of this organism. Note: the invertebrate clade is a catch all category that includes organisims not typically classified as invertebrate
    \n"; +printf "
    common nameLinks to an existing assembly browser, Button opens an assembly request form.
    \n"; +printf "
    scientific name (count)Links to Google image search. Count shows the number of assemblies available for this orgnism.
    \n"; +printf "
    NCBI assemblyLinks to NCBI resource record.
    \n"; +printf "
    assembly
    sizeNumber of nucleotides in the assembly.
    \n"; +printf "
    sequence
    countThe number of sequences in this assembly.
    \n"; +printf "
    scaffold N50
    length (L50)N50 (L50) length.
    \n"; +printf "
    contig N50
    length (L50)N50 (L50) length.
    \n"; +printf "
    IUCNLinks to IUCN Red List of Threatened Species (version 2021-3) CR - Critical / EN - Endangered / VU - Vulnerable
    \n", $statusColors{"CR"}, $statusColors{"EN"}, $statusColors{"VU"}; +printf "
    NCBI taxIDLinks to NCBI Taxonomy database.
    \n"; +printf "
    assembly
    dateDate submitted to NCBI assembly database.
    \n"; +printf "
    Assembly submitterPerson or group who submitted to <NCBI Assembly database.
    \n"; +printf "
    cladeClade of this organism. Note: the invertebrate clade is a catch all category that includes organisims not typically classified as invertebrate
    \n"; printf "\n"; printf "\n"; my %equivalentNamesUsed; # key is NCBI sciName, value is IUCN sciName my $pageSectionCount = 0; my %checkDupAsmId; # key is asmId, value is count of times seen my %cladeSciNameCounts; # key is clade, value is number of different # scientific names my %gcfGcaCounts; # key is GCF or GCA, value is count of each my $asmCountInTable = 0; # counting the rows output my %statusCounts; # key is status: CR EN VU, value is count my $totalAssemblySize = 0; # sum of all assembly sizes @@ -1031,36 +1031,36 @@ if (length($statusColor)) { if ($asmCountInTable > 500) { printf "", $rowClass, $statusColor; } else { printf "", $rowClass, $statusColor; } } else { if ($asmCountInTable > 500) { printf "", $rowClass; } else { printf "", $rowClass; } } ############# first column, common name link to browser or request button ## if (defined($comName{$asmId})) { - printf "%s", $browserUrl, $commonName; + printf "%s", $browserUrl, $commonName; } else { if (length($ucscDb)) { - printf "%s", $browserUrl, $commonName; + printf "%s", $browserUrl, $commonName; } else { - printf "", $asmId, $commonName; + printf "", $asmId, $commonName; } } printf PC "\t%s", $commonName; # output to clade.tableData.tsv ############# second column, scientific name and google image search ######### if (defined($sciNames{$asmId})) { my $noSpace = $sciNames{$asmId}; $noSpace =~ s/ /+/g; my $imgSearchUrl="https://images.google.com/images?q=$noSpace&um=1&hl=en&safe=active&nfpr=1&tbs=il:cl"; if ($assembliesAvailable > 1) { printf "%s (%s)", $imgSearchUrl, $sciNames{$asmId}, commify($assembliesAvailable); } else { printf "%s", $imgSearchUrl, $sciNames{$asmId}; } printf PC "\t%s", $sciNames{$asmId}; # output to clade.tableData.txt