From: Don Armstrong <don@donarmstrong.com>
Date: Fri, 6 Jan 2017 19:33:43 +0000 (-0800)
Subject: track aliases
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=cc72aef100329d6f16efb453b618c0f6dee43210;p=bin.git

track aliases
---

diff --git a/acro_gene b/acro_gene
index 46c9621..083dd0e 100755
--- a/acro_gene
+++ b/acro_gene
@@ -87,6 +87,7 @@ open($fh,'<',$options{gene_db}) or
 
 my @header;
 my %genes;
+my %aliases;
 while (<$fh>) {
     chomp;
     my @r = split /\t/;
@@ -97,11 +98,20 @@ while (<$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};
+    }
     print '\DeclareAcronym{'.
         $gene.'}{short=\href{http://www.genenames.org/cgi-bin/gene_symbol_report?match='.
         $gene.'}{'.$gene.'},long={'.$name.