#!/usr/bin/env perl # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute # Copyright [2016-2019] EMBL-European Bioinformatics Institute # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =cut # Script to update the documentation page "Data description". use strict; use warnings; use Getopt::Long; use JSON; # Print the usage instructions if run without parameters usage() unless (scalar(@ARGV)); my ($version,$git_dir,$input_file,$output_file,$help); GetOptions( 'version=i' => \$version, 'git_dir=s' => \$git_dir, 'i=s' => \$input_file, 'o=s' => \$output_file, 'help!' => \$help ); usage("Ensembl release version must be specified (-version)") unless ($version); usage("Path to the VEP_plugins directory must be specified (-git_dir)") unless ($git_dir); usage("VEP plugin documentation input file must be specified (-i)") unless ($input_file); usage("Output file must be specified (-o)") unless ($output_file); usage() if ($help); my ($content_before, $new_content, $content_after); my $tmp_file = 'vep_plugins_tmp.html'; my $vep_plugin_url = "https://github.com/Ensembl/VEP_plugins/"; my $vep_plugin_url_version = "https://github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]"; my $plugin_conf_file = "$git_dir/plugin_config.txt"; my $cpanm_url = 'https://metacpan.org/pod/'; my @files; my %data = (); my %data_section = (); my %plugins_to_skip = ( 'CCDSFilter.pm' => 1, 'CSN.pm' => 1, 'DAS.pm' => 1, 'GXA.pm' => 1, 'HGVSReferenceBase.pm' => 1, 'miRNA.pm' => 1, 'NonSynonymousFilter.pm' => 1, 'PolyPhen_SIFT.pm' => 1, 'RankFilter.pm' => 1, 'RefSeqHGVS.pm' => 1, ); my %class_colour = ( 'Conservation' => '#02599C', 'External ID' => '#333333', 'Frequency data' => '#FF7F50', 'HGVS' => '#9400D3', 'Look up' => '#006400', 'Nearby features' => '#E75480', # Dark pink 'ND' => 'darkgrey', 'Pathogenicity predictions' => '#1E90FF', 'Phenotype' => '#22949B', 'Sequence' => '#5F81A9', 'Splicing predictions' => 'red', 'Variant data' => '#B22222', 'Visualisation' => 'green', ); my %plugin_class = ( 'Downstream' => 'Nearby features', 'Draw' => 'Visualisation', 'FATHMM' => 'Pathogenicity predictions', 'FlagLRG' => 'External ID', 'GO' => 'Phenotype', 'G2P' => 'Phenotype', 'gnomADc' => 'Frequency data', 'HGVSIntronOffset' => 'HGVS', 'LocalID' => 'Look up', 'NearestExonJB' => 'Nearby features', 'NearestGene' => 'Nearby features', 'Phenotypes' => 'Phenotype', 'PON_P2' => 'Pathogenicity predictions', 'PostGAP' => 'Phenotype', 'ProteinSeqs' => 'Sequence', 'ReferenceQuality' => 'Sequence', 'SingleLetterAA' => 'HGVS', 'SubsetVCF' => 'Variant data', 'TSSDistance' => 'Nearby features', ); my %plugin_extended_names = ( 'CADD' => 'Combined Annotation Dependent Depletion', 'CSN' => 'Clinical Sequencing Nomenclature', 'DAS' => 'Distributed Annotation System', 'G2P' => 'gene2phenotype', 'GO' => 'Gene Ontology', 'LD' => 'Linkage Disequilibrium', 'LoFtool' => 'Loss-of-function', 'LOVD' => 'Leiden Open Variation Database', 'MPC' => 'missense deleteriousness metric', 'MTR' => 'Missense Tolerance Ratio', ); # Get information from some of the plugins open P, "< $plugin_conf_file" or die $!; my $plugin_name = ''; while(

) { chomp $_; if ($_ =~ /"key"\s=>\s"(.+)"/) { $plugin_name = $1; $data_section{$plugin_name} = (); } if ($_ =~ / "section" => "(.+)",/) { $data_section{$plugin_name}{'section'} = $1; } } close(P); # Parse each plugin to extract some information my $dh; opendir($dh,$git_dir) or die $!; while (my $file = readdir($dh)) { next if ($file !~ /\.pm$/ || $plugins_to_skip{$file}); push (@files, $file); read_plugin_file($file); $file =~ /^(.+)\.pm$/; my $p_name = $1; if ($plugin_class{$p_name}) { if ($data_section{$p_name}) { $data_section{$p_name}{'section'} = $plugin_class{$p_name}; } else { $data_section{$p_name} = {'section' => $plugin_class{$p_name}}; } } } # Print output HTML open OUT, "> $output_file" or die $!; my $table_content .= qq{ }; my @sorted_files = sort { lc $a cmp lc $b } @files; my $tr_class = 'bg1'; my %plugin_class_list; # 1 Plugin file <=> 1 row in the output table foreach my $file (@sorted_files) { print "Plugin: $file\n"; my $plugin_name = $data{$file}{'name'}; my $plugin_class = ($data_section{$plugin_name} && $data_section{$plugin_name}{'section'}) ? $data_section{$plugin_name}{'section'} : 'ND'; my $plugin_class_colour = $class_colour{$plugin_class} ? $class_colour{$plugin_class} : 'black'; my $plugin_id = lc($plugin_class); $plugin_id =~ s/ /_/g; $plugin_class_list{$plugin_class} = $plugin_id; $table_content .= sprintf( ''. ''. ''. ''. ''. ''. '', $tr_class, $plugin_id, "$vep_plugin_url_version/$file", $plugin_name, ($plugin_extended_names{$plugin_name}) ? '
'.$plugin_extended_names{$plugin_name}.'
' : '', $data{$file}{'desc'}, $plugin_class_colour, $plugin_class, ($data{$file}{'libs'} && scalar(keys(%{$data{$file}{'libs'}})) != 0) ? ((scalar(keys(%{$data{$file}{'libs'}})) > 1) ? '
  • '.join('
  • ',values(%{$data{$file}{'libs'}})).'
' : (values(%{$data{$file}{'libs'}}))[0]) : '-', scalar(@{$data{$file}{'developer'}}) > 1 ? '
  • '.join("
  • ",@{$data{$file}{'developer'}})."
" : $data{$file}{'developer'}->[0] ); $tr_class = ($tr_class eq 'bg1') ? 'bg2' : 'bg1'; $table_content .= "\n"; } $table_content .= qq{
Plugin Description Category External libraries Developer
%s%s
%s
%s%s
}; close(OUT); # Add a dropdown to select the plugins to display by category $new_content .= qq{

Select categories: \n
}; $new_content .= $table_content; # Replace the old HTML table by the new one, within the existing vep_plugins.html file my $section = 'Plugins list'; `cp $input_file $tmp_file`; $content_before = get_content($section,'start'); $content_after = get_content($section,'end'); print_into_tmp_file($tmp_file,$content_before,$new_content,$content_after); `cp $tmp_file $output_file`; `rm -f $tmp_file`; # Read and parse some information from the given plugin module # Mainly parse the perldoc content sub read_plugin_file { my $file = shift; my @developer = (); my $name = ''; my $desc = ''; my %libs; open F, "< $git_dir/$file" or die $!; while() { my $line = $_; chomp($line); # Get the developer information (i.e. if this has been developped by Ensembl or not) if ($line =~ /=head1 LICENSE/) { my $license_flag = 1; while ($license_flag != 0) { $line = ; chomp($line); if ($line =~ /^\s*=head1/ || $line =~ /^\s*=cut/) { $license_flag = 0; } else { @developer = ("Ensembl") if ($line =~ /Copyright\s+.+\s+EMBL-European\s+Bioinformatics\s+Institute/); } } } # Contact/developper information if ($line =~ /=head1 CONTACT/ && scalar(@developer) == 0) { my $contact_flag = 1; while ($contact_flag != 0) { $line = ; chomp($line); if ($line =~ /^\s*=head1/ || $line =~ /^\s*=cut/) { $contact_flag = 0; } else { $line =~ s/^\s+//; push(@developer, $1) if ($line =~ /(.+)\s+; chomp($line); if ($line =~ /^\s*=head1/ || $line =~ /^\s*=cut/) { $name_flag = 0; } else { $line =~ s/^\s+//; $name .= $1 if ($line =~ /(\S+)\s*/); } } } # Get the plugin description if ($line =~ /=head1 DESCRIPTION/) { my $desc_flag = 1; while ($desc_flag != 0) { $line = ; if ($line =~ /^\s*=head1/ || $line =~ /^\s*=cut/) { $desc_flag = 0; } else { if ($desc ne '' || $line !~ /^\s+$/) { if ($line =~ /^\s*\.\/(filter|vep)/ || $line =~ /^\s*--plugin/) { $line = '
'.$line.'
'; } else { $line =~ s/^\s+// if $line =~ /\S+/; } $desc .= $line; } } chomp($line); } } # Get the non Ensembl Perl module dependencies if ($line =~ /^use\s+(.+);/) { my $lib = $1; if ($lib !~ /^(strict|warnings)/ && $lib !~ /Bio\:\:EnsEMBL\:\:/) { $lib =~ /^(\S+)(.*)$/; $libs{$lib} = qq{$1$2}; } } } close(F); # Postprocess the description content (reformatting) $desc = "

$desc

"; $desc =~ s/\n\s*\n/<\/p>

/g; $desc =~ s/<\/p>

<\/p>/<\/p>/g; $desc =~ s/\n/
/g; $desc =~ s/
<\/p>/<\/p>/g; if ($desc =~ /<\/p>

/) { my $lc_name = lc($name); $lc_name =~ s/ /_/g; my $desc_link = qq{ ... more}; $desc =~ s/<\/p>

/$desc_link<\/p>

'; } $data{$file} = {'name' => $name, 'desc' => $desc, 'developer' => \@developer, 'libs' => \%libs}; } # Get the content of the existing vep_plugins.html file excluding the HTML table listing the plugins sub get_content { my $section = shift; my $type = shift; my $anchor = ""; my $line = `grep -m1 -n '$anchor' $tmp_file`; die "Can't find the anchor '$anchor' in the file" if (!$line || $line eq ''); $line =~ /^(\d+):/; my $line_number = $1; my $content; # Beginning to start anchor if ($type eq 'start') { $content = `head -n$line_number $tmp_file`; if ($content !~ /$anchor(\n?)$/) { $content = (split("$anchor", $content))[0].$anchor; } } # End anchor to end else { my $lines_count = (split(' ',`wc -l $tmp_file`))[0]; $line_number = $lines_count - $line_number + 1; $content = `tail -n$line_number $tmp_file`; if ($content !~ /^$anchor/) { $content = $anchor.(split("$anchor", $content))[1]; } } return $content; } # Recompose a new vep_plugins.html file with the new list of plugins sub print_into_tmp_file { my $tmp = shift; my $before = shift; my $new = shift; my $after = shift; open TMP, "> $tmp" or die $!; print TMP $before; print TMP $new; print TMP $after; } sub usage { my $msg = shift; print qq{ $msg Usage: perl update_web_vep_plugins_documentation.pl [OPTION] Update the page "vep_plugins.html" (under public-plugins/docs/htdocs/info/docs/tools/vep/script/). Options: -help Print this message -v Ensembl version, e.g. 65 (Required) -i Input file, e.g. vep_plugins.html (Required) -o Output file (Required) -git_dir Path to the VEP_plugins repository - used to fetch information about the VEP plugins (Required) } . "\n"; exit(0); }