src/hg/utils/automation/EnsGeneAutomate.pm 1.19

Index: src/hg/utils/automation/EnsGeneAutomate.pm
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/EnsGeneAutomate.pm,v
retrieving revision 1.18
retrieving revision 1.19
diff -b -B -U 4 -r1.18 -r1.19
--- src/hg/utils/automation/EnsGeneAutomate.pm	14 Jul 2009 22:26:08 -0000	1.18
+++ src/hg/utils/automation/EnsGeneAutomate.pm	6 Aug 2009 18:22:56 -0000	1.19
@@ -47,8 +47,9 @@
 $verToDate[49] = "mar2008";
 $verToDate[50] = "jul2008";
 $verToDate[51] = "nov2008";
 $verToDate[52] = "dec2008";
+$verToDate[54] = "may2009";
 $verToDate[55] = "jul2009";
 
 #	older versions for archive purposes, there are different
 #	directory structures for these, thus, the full path name
@@ -878,8 +879,24 @@
 'xenTro2' => 'xenopus_tropicalis_core_52_41l',
 );
 
 # key is UCSC db name, result is FTP file name under the gtf directory
+my %ensGeneGtfFileNames_54 = (
+'hg18' => 'homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz',
+);
+
+# key is UCSC db name, result is FTP file name under the fasta directory
+my %ensGeneFtpPeptideFileNames_54 = (
+'hg18' => 'homo_sapiens/pep/Homo_sapiens.NCBI36.54.pep.all.fa.gz',
+);
+
+#	directory name under release-50/mysql/ to find 'seq_region' and
+#	'assembly' table copies for GeneScaffold coordinate conversions
+my %ensGeneFtpMySqlFileNames_54 = (
+'hg18' => 'homo_sapiens_core_54_36p',
+);
+
+# key is UCSC db name, result is FTP file name under the gtf directory
 my %ensGeneGtfFileNames_55 = (
 'aedAeg0' => 'aedes_aegypti/Aedes_aegypti.AaegL1.55.gtf.gz',
 'anoCar1' => 'anolis_carolinensis/Anolis_carolinensis.AnoCar1.0.55.gtf.gz',
 'anoGam2' => 'anopheles_gambiae/Anopheles_gambiae.AgamP3.55.gtf.gz',
@@ -1040,11 +1057,12 @@
 'vicPac1' => 'vicugna_pacos_core_55_1c',
 'xenTro2' => 'xenopus_tropicalis_core_55_41n',
 );
 
-my @versionList = qw( 55 52 51 50 49 48 47 46 35 );
+my @versionList = qw( 55 54 52 51 50 49 48 47 46 35 );
 
 my @ensGtfReference;
+$ensGtfReference[54] = \%ensGeneGtfFileNames_54;
 $ensGtfReference[55] = \%ensGeneGtfFileNames_55;
 $ensGtfReference[52] = \%ensGeneGtfFileNames_52;
 $ensGtfReference[51] = \%ensGeneGtfFileNames_51;
 $ensGtfReference[50] = \%ensGeneGtfFileNames_50;
@@ -1053,8 +1071,9 @@
 $ensGtfReference[47] = \%ensGeneGtfFileNames_47;
 $ensGtfReference[46] = \%ensGeneGtfFileNames_46;
 $ensGtfReference[35] = \%ensGeneGtfFileNames_35;
 my @ensPepReference;
+$ensPepReference[54] = \%ensGeneFtpPeptideFileNames_54;
 $ensPepReference[55] = \%ensGeneFtpPeptideFileNames_55;
 $ensPepReference[52] = \%ensGeneFtpPeptideFileNames_52;
 $ensPepReference[51] = \%ensGeneFtpPeptideFileNames_51;
 $ensPepReference[50] = \%ensGeneFtpPeptideFileNames_50;
@@ -1063,8 +1082,9 @@
 $ensPepReference[47] = \%ensGeneFtpPeptideFileNames_47;
 $ensPepReference[46] = \%ensGeneFtpPeptideFileNames_46;
 $ensPepReference[35] = \%ensGeneFtpPeptideFileNames_35;
 my @ensMySqlReference;
+$ensMySqlReference[54] = \%ensGeneFtpMySqlFileNames_54;
 $ensMySqlReference[55] = \%ensGeneFtpMySqlFileNames_55;
 $ensMySqlReference[52] = \%ensGeneFtpMySqlFileNames_52;
 $ensMySqlReference[51] = \%ensGeneFtpMySqlFileNames_51;
 $ensMySqlReference[50] = \%ensGeneFtpMySqlFileNames_50;