use the new format for capture in remember-mail

[bin.git] / acro_gene

diff --git a/acro_gene b/acro_gene
index 46c9621efcba528407f3ed41226b3bc8a0f827aa..9a6968487f22e3d44f41ee483dcfd196d080f7d3 100755 (executable)
--- a/acro_gene
+++ b/acro_gene
@@ -87,6 +87,7 @@ open($fh,'<',$options{gene_db}) or
 
 my @header;
 my %genes;
+my %aliases;
 while (<$fh>) {
     chomp;
     my @r = split /\t/;
@@ -97,15 +98,27 @@ while (<$fh>) {
     my %r;
     @r{@header} = @r;
     $genes{$r{symbol}} = $r{name};
+    my $alias = $r{alias_symbol};
+    $alias =~ s/"//g;
+    my @aliases = split /\|/,$alias;
+    $aliases{@aliases} = ($r{name}) x @aliases;
 }
 
 for (@ARGV) {
     my $gene = $_;
     my $name = $genes{$gene};
+    if (not defined $name) {
+        $gene = $aliases{$gene};
+        next unless defined $gene;
+        $name = $genes{$gene};
+    }
+    my $url = 'http://www.genenames.org/cgi-bin/gene_symbol_report?match='.$gene;
     print '\DeclareAcronym{'.
-        $gene.'}{short=\href{http://www.genenames.org/cgi-bin/gene_symbol_report?match='.
-        $gene.'}{'.$gene.'},long={'.$name.
-        '},first-style=reversed}'."\n";
+        $gene.'}{short=\href{'.$url.
+        '}{\textit{'.$gene.'}},long={'.$name.
+        '},first-style=reversed,single={'.
+        '\href{'.$url.'}{\textit{'.$gene.'}} ('.$name.')'.
+        '}}'."\n";
 }