#!/usr/bin/perl use strict; use warnings; use Switch; use Cwd; use LWP::UserAgent qw(); #### This script parses html pathway output from PathVisio into the MediaWiki ImageMap format #### (http://www.mediawiki.org/wiki/Extension:ImageMap). It also changes hyperlinks, so that #### any Entrez ID links to the corresponding Gene Wiki entry using the Gene Wiki Entrez Linker #### plugin (http://plugins.gnf.org/cgi-bin/wp.cgi). Hyperlinks for other IDs are changed to #### point to the corresponding entry at the resource. #### This script is specifically designed to process human pathways only. #### Input #### Single html file, folder containing backpage information (titled "backpage"). #### The html file and backpage folder need to be in the same directory #### Output #### new text file with imagemap and wiki template syntax, with added extension ".txt" ## Define links to resources my $genewiki = "http://plugins.biogps.org/cgi-bin/wp.cgi?id="; my $chebi = "http://www.ebi.ac.uk/chebi/searchId=CHEBI:"; my $hmdb = "http://www.hmdb.ca/metabolites/"; my $cas = "http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno="; my $ensembl = "http://www.ensembl.org/Homo_sapiens/Search/Summary?_q="; my $uniprot = "http://www.expasy.org/uniprot/"; my $unigene = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=1548618&SEARCH="; my $keggcomp = "http://www.genome.jp/dbget-bin/www_bget?cpd:"; my $hugo = "http://www.genenames.org/data/hgnc_data.php?hgnc_id="; my $ec = "http://www.brenda-enzymes.info/php/result_flat.php4?ecno="; my $wikipedia = "http://en.wikipedia.org/wiki/"; my $wikipathways = "http://www.wikipathways.org/index.php/Pathway:"; #my $chembl = "https://www.ebi.ac.uk/chembldb/index.php/compound/inspect/"; ## CHEMBL identifiers are not properly exported by html exporter yet #### Find file my $html = <*.html>; my $pathway = (split('\.', $html))[0]; #### Define output file my $outfile = $html.".txt"; unless ( open(OUTFILE, ">$outfile") ) { #Open failed print "could not open file $outfile\n"; exit; } #### Process the file print "Processing pathway $pathway\n"; unless ( open(HTML, $html) ) { # Open failed print "could not open file $html\n"; exit; } $pathway =~ /.*_(WP\d*)$/; my $WPID = $1; #variable for width of png image my $imgWidth = 0; my $imgHeight = 0; my %seen = (); my @linkArray = (); my $color; print OUTFILE "\n\n"; print OUTFILE "{{Documentation|Template:Interactive_pathway_maps\/doc}}<\/noinclude>{{{header|\'\'Click on genes, proteins and metabolites below to link to respective articles.\'\' The interactive pathway map can be edited at WikiPathways: {{cite web | url = http:\/\/www.wikipathways.org\/index.php\/Pathway:$WPID | title = $pathway | author = | date = | work = | publisher = | pages = | accessdate = }} }}}\n\n
\n\n"; while (my $line = ) { if (!($line =~ m/href/)) { if ($line =~ m/image/) { $line =~ s/<\/IMG>/|right|alt=/; $imgWidth = $1; $imgHeight = $2; print OUTFILE "{{Preview Crop\n|Image={{Annotated image |float=none|image-width=".$imgWidth."|annot-color=white|imagemap=\n"; chomp $line; $line .= $pathway; $line .="\n"; } else{ $line =~ s/<\/MAP><\/BODY><\/HTML>//; } print OUTFILE "$line"; } elsif ($line =~ m/href/) { if ($line =~ m/^/) # remove trailing syntax in first line { $line =~ s///; } $line =~ m/href="(.+)" alt/; my $link = $1; $link =~ m/backpage\/(.+).html/; my $xref = $1; $xref =~ m/(.+)_/; my $system = $1; my $newlink = ""; my $id = ""; $color = 'red'; switch($system) { case "L" { #print "system is Entrez\n"; $xref =~ m/L_(.+)/; $id = $1; $newlink = $genewiki.$id; $newlink = FetchArticleURL($newlink); if ($newlink =~ m/Special:Search/) { $color = 'red'; $newlink =~ s/#Interactive_pathway_map go to/ search for/; } else { $newlink =~ m/wiki\/(.+)#Interactive/; $id = $1; $color = 'blue'; } } case "EnHs" { #print "system is Ensembl\n"; $xref =~ m/EnHs_(.+)/; $id = $1; my $entrez = BackpageLookup($xref, 'Entrez Gene'); #Use full Xref since that's the name of the backpage file if ($entrez eq "null") { $newlink = $ensembl.$id." Go to Ensembl"; $color = 'green'; } else { $id = $entrez; $newlink = $genewiki.$id; $newlink = FetchArticleURL($newlink); if ($newlink =~ m/Special:Search/) { $color = 'red'; $newlink =~ s/#Interactive_pathway_map go to/ search for/; } else { $newlink =~ m/wiki\/(.+)#Interactive/; $id = $1; $color = 'blue'; } } } case "S" { #print "system is Uniprot\n"; $xref =~ m/S_(.+)/; $id = $1; my $entrez = BackpageLookup($xref, 'Entrez Gene'); #Use full Xref since that's the name of the backpage file if ($entrez eq "null") { $newlink = $uniprot.$id." Go to UniProt"; $color = 'green'; } else { $id = $entrez; $newlink = $genewiki.$id; $newlink = FetchArticleURL($newlink); if ($newlink =~ m/Special:Search/) { $color = 'red'; $newlink =~ s/#Interactive_pathway_map go to/ search for/; } else { $newlink =~ m/wiki\/(.+)#Interactive/; $id = $1; $color = 'blue'; } } } case "U" { #print "system is Unigene\n"; $xref =~ m/U_(.+)/; $id = $1; my $entrez = BackpageLookup($xref, 'Entrez Gene'); #Use full Xref since that's the name of the backpage file if ($entrez eq "null") { $newlink = $unigene.$id." Go to UniGene"; $color = 'green'; } else { $id = $entrez; $newlink = $genewiki.$id; $newlink = FetchArticleURL($newlink); if ($newlink =~ m/Special:Search/){ $color = 'red'; $newlink =~ s/#Interactive_pathway_map go to/ search for/; } else { $newlink =~ m/wiki\/(.+)#Interactive/; $id = $1; $color = 'blue'; } } } case "H" { #print "system is HUGO\n"; $xref =~ m/H_(.+)/; $id = $1; my $entrez = BackpageLookup($xref, 'Entrez Gene'); #Use full Xref since that's the name of the backpage file if ($entrez eq "null") { $newlink = $hugo.$id." Go to HGNC"; $color = 'green'; } else { $id = $entrez; $newlink = $genewiki.$id; $newlink = FetchArticleURL($newlink); if ($newlink =~ m/Special:Search/){ $color = 'red'; $newlink =~ s/#Interactive_pathway_map go to/ search for/; } else { $newlink =~ m/wiki\/(.+)#Interactive/; $id = $1; $color = 'blue'; } } } case "Ch" { #print "system is HMDB\n"; $xref =~ /^Ch_(HMDB\d+)$/; $id = $1; my $wp = BackpageLookup($xref, 'Wikipedia'); if ($wp eq "null"){ $newlink = $hmdb.$id." Go to HMDB"; $color = 'green'; } else { $id = $wp; $newlink = $wikipedia.$wp." Go to article"; $color = 'blue'; } } case "Ca" { #print "system is CAS\n"; $xref =~ m/Ca_(.+)/; $id = $1; my $wp = BackpageLookup($xref, 'Wikipedia'); if ($wp eq "null"){ $newlink = $cas.$id." Go to CAS"; $color = 'green'; } else { $id = $wp; $newlink = $wikipedia.$wp." Go to article"; $color = 'blue'; } } case "Ck" { #print "system is KEGG compound\n"; $xref =~ m/Ck_(.+)/; $id = $1; my $wp = BackpageLookup($xref, 'Wikipedia'); if ($wp eq "null"){ $newlink = $keggcomp.$id." Go to KEGG"; $color = 'green'; } else { $id = $wp; $newlink = $wikipedia.$wp." Go to article"; $color = 'blue'; } } # case "ChEMBL" # { # $xref =~ /_(CHEMBL\d+)$/; # $id = $1; # my $wp = BackpageLookup($xref, 'Wikipedia'); # if ($wp eq "null"){ # $newlink = $chembl.$id." Go to ChEMBL"; # $color = 'green'; # } # else { # $id = $wp; # $newlink = $wikipedia.$wp." Go to article"; # $color = 'blue'; # } # } case "E" { #print "system is EC\n"; $xref =~ m/E_(.+)/; $id = $1; $newlink = $ec.$id." Go to BRENDA"; $color = 'green'; } case "Wp" { #print "system is WikiPathways\n"; $xref =~ m/Wp_(.+)/; $id = $1; $newlink = $wikipathways.$id." Go to WikiPathways"; $color = 'green'; } case "enzyme" { #print "system is EC\n"; $xref =~ m/enzyme_(.+)/; $id = $1; $newlink = $ec.$id." Go to BRENDA"; $color = 'green'; } else { print "undefined system found: $system\n"; } } #remove #interactive_pathway_map anchor from links $newlink =~ s/#Interactive_pathway_map//; #make unique references to copies if ($seen{$id}++){ my $alt = $seen{$id} - 1; $id = $id."__alt".$alt; } $line =~ m/coords="(\d+\.\d+),(\d+\.\d+),(\d+\.\d+),(\d+\.\d+)/; my @links = ($1, $2, $3, $4, $color, $id); push @linkArray, [@links]; $line =~ s/\n|annotations=\n"; #color link lines for my $i ( 0 .. $#linkArray ) { my $left = $linkArray[$i][0]; my $right = $imgWidth - $left + 5; my $top = $linkArray[$i][3] -15;# -$i*1; my $width = $linkArray[$i][2] - $linkArray[$i][0]; my $color = $linkArray[$i][4]; print OUTFILE "{{Annotation|0|0|[[
]]}}\n"; } #switch to highlight per gene print OUTFILE "{{#switch:{{{highlight}}}\n"; for my $i ( 0 .. $#linkArray ) { my $left = $linkArray[$i][0]; my $width = $linkArray[$i][2] - $linkArray[$i][0] - 7; my $height = $linkArray[$i][3] - $linkArray[$i][1] - 8; my $top = $linkArray[$i][1] - 12; my $color = 'black'; my $key = $linkArray[$i][5]; print OUTFILE "|".$key."=\n"; print OUTFILE "{{Annotation|0|0|[[
]]}}\n"; } print OUTFILE "}}\n"; print OUTFILE "|caption=\n}}\n|bsize=\n"; #crop variables my $cwidth = 375; my $cheight = 350; my $otop = 25; my $oleft = 10; print OUTFILE "|cWidth={{#switch:{{{highlight}}}\n"; for my $i ( 0 .. $#linkArray ) { my $key = $linkArray[$i][5]; print OUTFILE "|".$key."=".$cwidth."\n"; } print OUTFILE "|#default=$imgWidth\n}}\n"; print OUTFILE "|cHeight={{#switch:{{{highlight}}}\n"; for my $i ( 0 .. $#linkArray ) { my $key = $linkArray[$i][5]; print OUTFILE "|".$key."=".$cheight."\n"; } print OUTFILE "|#default=$imgHeight\n}}\n"; print OUTFILE "|oTop={{#switch:{{{highlight}}}\n"; for my $i ( 0 .. $#linkArray ) { my $key = $linkArray[$i][5]; my $min = $otop; my $max = $imgHeight - $cheight + $min; my $offset = $linkArray[$i][3] + $min - ($cheight / 2) - (($linkArray[$i][3] - $linkArray[$i][1]) / 2); if ($offset > $max){ $offset = $max; } if ($offset < $min ){ $offset = $min; } print OUTFILE "|".$key."=$offset\n"; } print OUTFILE "|#default=".$otop."\n}}\n"; print OUTFILE "|oLeft={{#switch:{{{highlight}}}\n"; for my $i ( 0 .. $#linkArray ) { my $key = $linkArray[$i][5]; my $min = $oleft; my $max = $imgWidth - $cwidth + $min; my $offset = $linkArray[$i][0] + $min - ($cwidth / 2) + (($linkArray[$i][2] - $linkArray[$i][0]) / 2); if ($offset > $max){ $offset = $max; } if ($offset < $min ){ $offset = $min; } print OUTFILE "|".$key."=$offset\n"; } print OUTFILE "|#default=".$oleft."\n}}\n"; print OUTFILE "|Location=left\n|Description=".$pathway." [http:\/\/www.wikipathways.org\/index.php\/Pathway:$WPID edit]\n}}\n
{{reflist}}[[Category:WikiPathways]]"; close OUTFILE; close HTML; print "\n\n\nDone!\n\n"; sub BackpageLookup { my ($xref, $system) = @_; chdir("backpage"); my $dir = getcwd; print "Directory is: $dir\n"; my $hit = "null"; my $backpage = $xref.".html"; unless ( open(BACK, $backpage) ) { # Open failed print "could not open file $backpage\n"; exit; } while (my $line = ) { if ($line =~ m/<\/a>, $system
(.+?)<\/a>, $system
new; my $response = $ua->get($newlink); $newlink = $response->request->url."#Interactive_pathway_map go to article"; return $newlink; }