src/hg/utils/automation/EnsGeneAutomate.pm 1.18
1.18 2009/07/14 22:26:08 hiram
Updated with version 55 gene set pointers
Index: src/hg/utils/automation/EnsGeneAutomate.pm
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/EnsGeneAutomate.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -b -B -U 4 -r1.17 -r1.18
--- src/hg/utils/automation/EnsGeneAutomate.pm 4 Feb 2009 18:34:49 -0000 1.17
+++ src/hg/utils/automation/EnsGeneAutomate.pm 14 Jul 2009 22:26:08 -0000 1.18
@@ -47,8 +47,9 @@
$verToDate[49] = "mar2008";
$verToDate[50] = "jul2008";
$verToDate[51] = "nov2008";
$verToDate[52] = "dec2008";
+$verToDate[55] = "jul2009";
# older versions for archive purposes, there are different
# directory structures for these, thus, the full path name
# to append to the release-NN/ top level directory.
@@ -876,11 +877,175 @@
'vicPac1' => 'vicugna_pacos_core_52_1a',
'xenTro2' => 'xenopus_tropicalis_core_52_41l',
);
-my @versionList = qw( 52 51 50 49 48 47 46 35 );
+# 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',
+'bosTau4' => 'bos_taurus/Bos_taurus.Btau_4.0.55.gtf.gz',
+'ce7' => 'caenorhabditis_elegans/Caenorhabditis_elegans.WS200.55.gtf.gz',
+'canFam2' => 'canis_familiaris/Canis_familiaris.BROADD2.55.gtf.gz',
+'cavPor3' => 'cavia_porcellus/Cavia_porcellus.cavPor3.55.gtf.gz',
+'choHof1' => 'choloepus_hoffmanni/Choloepus_hoffmanni.choHof1.55.gtf.gz',
+'ci2' => 'ciona_intestinalis/Ciona_intestinalis.JGI2.55.gtf.gz',
+'cioSav2' => 'ciona_savignyi/Ciona_savignyi.CSAV2.0.55.gtf.gz',
+'danRer6' => 'danio_rerio/Danio_rerio.Zv8.55.gtf.gz',
+'dasNov2' => 'dasypus_novemcinctus/Dasypus_novemcinctus.dasNov2.55.gtf.gz',
+'dipOrd1' => 'dipodomys_ordii/Dipodomys_ordii.dipOrd1.55.gtf.gz',
+'dm5' => 'drosophila_melanogaster/Drosophila_melanogaster.BDGP5.4.55.gtf.gz',
+'echTel1' => 'echinops_telfairi/Echinops_telfairi.TENREC.55.gtf.gz',
+'equCab2' => 'equus_caballus/Equus_caballus.EquCab2.55.gtf.gz',
+'eriEur1' => 'erinaceus_europaeus/Erinaceus_europaeus.HEDGEHOG.55.gtf.gz',
+'felCat3' => 'felis_catus/Felis_catus.CAT.55.gtf.gz',
+'galGal3' => 'gallus_gallus/Gallus_gallus.WASHUC2.55.gtf.gz',
+'gasAcu1' => 'gasterosteus_aculeatus/Gasterosteus_aculeatus.BROADS1.55.gtf.gz',
+'gorGor1' => 'gorilla_gorilla/Gorilla_gorilla.gorGor1.55.gtf.gz',
+'hg19' => 'homo_sapiens/Homo_sapiens.GRCh37.55.gtf.gz',
+'loxAfr2' => 'loxodonta_africana/Loxodonta_africana.loxAfr2.55.gtf.gz',
+'rheMac2' => 'macaca_mulatta/Macaca_mulatta.MMUL_1.55.gtf.gz',
+'macEug1' => 'macropus_eugenii/Macropus_eugenii.Meug_1.0.55.gtf.gz',
+'micMur1' => 'microcebus_murinus/Microcebus_murinus.micMur1.55.gtf.gz',
+'monDom5' => 'monodelphis_domestica/Monodelphis_domestica.BROADO5.55.gtf.gz',
+'mm9' => 'mus_musculus/Mus_musculus.NCBIM37.55.gtf.gz',
+'myoLuc1' => 'myotis_lucifugus/Myotis_lucifugus.MICROBAT1.55.gtf.gz',
+'ochPri2' => 'ochotona_princeps/Ochotona_princeps.pika.55.gtf.gz',
+'ornAna1' => 'ornithorhynchus_anatinus/Ornithorhynchus_anatinus.OANA5.55.gtf.gz',
+'oryCun1' => 'oryctolagus_cuniculus/Oryctolagus_cuniculus.RABBIT.55.gtf.gz',
+'oryLat2' => 'oryzias_latipes/Oryzias_latipes.MEDAKA1.55.gtf.gz',
+'otoGar1' => 'otolemur_garnettii/Otolemur_garnettii.BUSHBABY1.55.gtf.gz',
+'panTro2' => 'pan_troglodytes/Pan_troglodytes.CHIMP2.1.55.gtf.gz',
+'ponAbe2' => 'pongo_pygmaeus/Pongo_pygmaeus.PPYG2.55.gtf.gz',
+'proCap1' => 'procavia_capensis/Procavia_capensis.proCap1.55.gtf.gz',
+'pteVam1' => 'pteropus_vampyrus/Pteropus_vampyrus.pteVam1.55.gtf.gz',
+'rn4' => 'rattus_norvegicus/Rattus_norvegicus.RGSC3.4.55.gtf.gz',
+'sacCer2' => 'saccharomyces_cerevisiae/Saccharomyces_cerevisiae.SGD1.01.55.gtf.gz',
+'sorAra1' => 'sorex_araneus/Sorex_araneus.COMMON_SHREW1.55.gtf.gz',
+'speTri1' => 'spermophilus_tridecemlineatus/Spermophilus_tridecemlineatus.SQUIRREL.55.gtf.gz',
+'taeGut1' => 'taeniopygia_guttata/Taeniopygia_guttata.taeGut3.2.4.55.gtf.gz',
+'fr2' => 'takifugu_rubripes/Takifugu_rubripes.FUGU4.55.gtf.gz',
+'tarSyr1' => 'tarsius_syrichta/Tarsius_syrichta.tarSyr1.55.gtf.gz',
+'tetNig2' => 'tetraodon_nigroviridis/Tetraodon_nigroviridis.TETRAODON8.55.gtf.gz',
+'tupBel1' => 'tupaia_belangeri/Tupaia_belangeri.TREESHREW.55.gtf.gz',
+'turTru1' => 'tursiops_truncatus/Tursiops_truncatus.turTru1.55.gtf.gz',
+'vicPac1' => 'vicugna_pacos/Vicugna_pacos.vicPac1.55.gtf.gz',
+'xenTro2' => 'xenopus_tropicalis/Xenopus_tropicalis.JGI4.1.55.gtf.gz',
+);
+
+# key is UCSC db name, result is FTP file name under the fasta directory
+my %ensGeneFtpPeptideFileNames_55 = (
+'aedAeg0' => 'aedes_aegypti/pep/Aedes_aegypti.AaegL1.55.pep.all.fa.gz',
+'anoCar1' => 'anolis_carolinensis/pep/Anolis_carolinensis.AnoCar1.0.55.pep.all.fa.gz',
+'anoGam2' => 'anopheles_gambiae/pep/Anopheles_gambiae.AgamP3.55.pep.all.fa.gz',
+'bosTau4' => 'bos_taurus/pep/Bos_taurus.Btau_4.0.55.pep.all.fa.gz',
+'ce7' => 'caenorhabditis_elegans/pep/Caenorhabditis_elegans.WS200.55.pep.all.fa.gz',
+'canFam2' => 'canis_familiaris/pep/Canis_familiaris.BROADD2.55.pep.all.fa.gz',
+'cavPor3' => 'cavia_porcellus/pep/Cavia_porcellus.cavPor3.55.pep.all.fa.gz',
+'choHof1' => 'choloepus_hoffmanni/pep/Choloepus_hoffmanni.choHof1.55.pep.all.fa.gz',
+'ci2' => 'ciona_intestinalis/pep/Ciona_intestinalis.JGI2.55.pep.all.fa.gz',
+'cioSav2' => 'ciona_savignyi/pep/Ciona_savignyi.CSAV2.0.55.pep.all.fa.gz',
+'danRer6' => 'danio_rerio/pep/Danio_rerio.Zv8.55.pep.all.fa.gz',
+'dasNov2' => 'dasypus_novemcinctus/pep/Dasypus_novemcinctus.dasNov2.55.pep.all.fa.gz',
+'dipOrd1' => 'dipodomys_ordii/pep/Dipodomys_ordii.dipOrd1.55.pep.all.fa.gz',
+'dm5' => 'drosophila_melanogaster/pep/Drosophila_melanogaster.BDGP5.4.55.pep.all.fa.gz',
+'echTel1' => 'echinops_telfairi/pep/Echinops_telfairi.TENREC.55.pep.all.fa.gz',
+'equCab2' => 'equus_caballus/pep/Equus_caballus.EquCab2.55.pep.all.fa.gz',
+'eriEur1' => 'erinaceus_europaeus/pep/Erinaceus_europaeus.HEDGEHOG.55.pep.all.fa.gz',
+'felCat3' => 'felis_catus/pep/Felis_catus.CAT.55.pep.all.fa.gz',
+'galGal3' => 'gallus_gallus/pep/Gallus_gallus.WASHUC2.55.pep.all.fa.gz',
+'gasAcu1' => 'gasterosteus_aculeatus/pep/Gasterosteus_aculeatus.BROADS1.55.pep.all.fa.gz',
+'gorGor1' => 'gorilla_gorilla/pep/Gorilla_gorilla.gorGor1.55.pep.all.fa.gz',
+'hg19' => 'homo_sapiens/pep/Homo_sapiens.GRCh37.55.pep.all.fa.gz',
+'loxAfr2' => 'loxodonta_africana/pep/Loxodonta_africana.loxAfr2.55.pep.all.fa.gz',
+'rheMac2' => 'macaca_mulatta/pep/Macaca_mulatta.MMUL_1.55.pep.all.fa.gz',
+'macEug1' => 'macropus_eugenii/pep/Macropus_eugenii.Meug_1.0.55.pep.all.fa.gz',
+'micMur1' => 'microcebus_murinus/pep/Microcebus_murinus.micMur1.55.pep.all.fa.gz',
+'monDom5' => 'monodelphis_domestica/pep/Monodelphis_domestica.BROADO5.55.pep.all.fa.gz',
+'mm9' => 'mus_musculus/pep/Mus_musculus.NCBIM37.55.pep.all.fa.gz',
+'myoLuc1' => 'myotis_lucifugus/pep/Myotis_lucifugus.MICROBAT1.55.pep.all.fa.gz',
+'ochPri2' => 'ochotona_princeps/pep/Ochotona_princeps.pika.55.pep.all.fa.gz',
+'ornAna1' => 'ornithorhynchus_anatinus/pep/Ornithorhynchus_anatinus.OANA5.55.pep.all.fa.gz',
+'oryCun1' => 'oryctolagus_cuniculus/pep/Oryctolagus_cuniculus.RABBIT.55.pep.all.fa.gz',
+'oryLat2' => 'oryzias_latipes/pep/Oryzias_latipes.MEDAKA1.55.pep.all.fa.gz',
+'otoGar1' => 'otolemur_garnettii/pep/Otolemur_garnettii.BUSHBABY1.55.pep.all.fa.gz',
+'panTro2' => 'pan_troglodytes/pep/Pan_troglodytes.CHIMP2.1.55.pep.all.fa.gz',
+'ponAbe2' => 'pongo_pygmaeus/pep/Pongo_pygmaeus.PPYG2.55.pep.all.fa.gz',
+'proCap1' => 'procavia_capensis/pep/Procavia_capensis.proCap1.55.pep.all.fa.gz',
+'pteVam1' => 'pteropus_vampyrus/pep/Pteropus_vampyrus.pteVam1.55.pep.all.fa.gz',
+'rn4' => 'rattus_norvegicus/pep/Rattus_norvegicus.RGSC3.4.55.pep.all.fa.gz',
+'sacCer2' => 'saccharomyces_cerevisiae/pep/Saccharomyces_cerevisiae.SGD1.01.55.pep.all.fa.gz',
+'sorAra1' => 'sorex_araneus/pep/Sorex_araneus.COMMON_SHREW1.55.pep.all.fa.gz',
+'speTri1' => 'spermophilus_tridecemlineatus/pep/Spermophilus_tridecemlineatus.SQUIRREL.55.pep.all.fa.gz',
+'taeGut1' => 'taeniopygia_guttata/pep/Taeniopygia_guttata.taeGut3.2.4.55.pep.all.fa.gz',
+'fr2' => 'takifugu_rubripes/pep/Takifugu_rubripes.FUGU4.55.pep.all.fa.gz',
+'tarSyr1' => 'tarsius_syrichta/pep/Tarsius_syrichta.tarSyr1.55.pep.all.fa.gz',
+'tetNig2' => 'tetraodon_nigroviridis/pep/Tetraodon_nigroviridis.TETRAODON8.55.pep.all.fa.gz',
+'tupBel1' => 'tupaia_belangeri/pep/Tupaia_belangeri.TREESHREW.55.pep.all.fa.gz',
+'turTru1' => 'tursiops_truncatus/pep/Tursiops_truncatus.turTru1.55.pep.all.fa.gz',
+'vicPac1' => 'vicugna_pacos/pep/Vicugna_pacos.vicPac1.55.pep.all.fa.gz',
+'xenTro2' => 'xenopus_tropicalis/pep/Xenopus_tropicalis.JGI4.1.55.pep.all.fa.gz',
+);
+
+# directory name under release-50/mysql/ to find 'seq_region' and
+# 'assembly' table copies for GeneScaffold coordinate conversions
+my %ensGeneFtpMySqlFileNames_55 = (
+'aedAeg0' => 'aedes_aegypti_core_55_1d',
+'anoCar1' => 'anolis_carolinensis_core_55_1a',
+'anoGam2' => 'anopheles_gambiae_core_55_3k',
+'bosTau4' => 'bos_taurus_core_55_4e',
+'ce7' => 'caenorhabditis_elegans_core_55_200',
+'canFam2' => 'canis_familiaris_core_55_2m',
+'cavPor3' => 'cavia_porcellus_core_55_3a',
+'choHof1' => 'choloepus_hoffmanni_core_55_1a',
+'ci2' => 'ciona_intestinalis_core_55_2m',
+'cioSav2' => 'ciona_savignyi_core_55_2h',
+'danRer6' => 'danio_rerio_core_55_8e',
+'dasNov2' => 'dasypus_novemcinctus_core_55_2a',
+'dipOrd1' => 'dipodomys_ordii_core_55_1c',
+'dm5' => 'drosophila_melanogaster_core_55_54c',
+'echTel1' => 'echinops_telfairi_core_55_1g',
+'equCab2' => 'equus_caballus_core_55_2d',
+'eriEur1' => 'erinaceus_europaeus_core_55_1e',
+'felCat3' => 'felis_catus_core_55_1f',
+'galGal3' => 'gallus_gallus_core_55_2m',
+'gasAcu1' => 'gasterosteus_aculeatus_core_55_1j',
+'gorGor1' => 'gorilla_gorilla_core_55_1',
+'hg19' => 'homo_sapiens_core_55_37',
+'loxAfr2' => 'loxodonta_africana_core_55_2a',
+'rheMac2' => 'macaca_mulatta_core_55_10l',
+'macEug1' => 'macropus_eugenii_core_55_1',
+'micMur1' => 'microcebus_murinus_core_55_1b',
+'monDom5' => 'monodelphis_domestica_core_55_5i',
+'mm9' => 'mus_musculus_core_55_37h',
+'myoLuc1' => 'myotis_lucifugus_core_55_1g',
+'ochPri2' => 'ochotona_princeps_core_55_1c',
+'ornAna1' => 'ornithorhynchus_anatinus_core_55_1k',
+'oryCun1' => 'oryctolagus_cuniculus_core_55_1h',
+'oryLat2' => 'oryzias_latipes_core_55_1i',
+'otoGar1' => 'otolemur_garnettii_core_55_1e',
+'panTro2' => 'pan_troglodytes_core_55_21l',
+'ponAbe2' => 'pongo_pygmaeus_core_55_1c',
+'proCap1' => 'procavia_capensis_core_55_1c',
+'pteVam1' => 'pteropus_vampyrus_core_55_1c',
+'rn4' => 'rattus_norvegicus_core_55_34w',
+'sacCer2' => 'saccharomyces_cerevisiae_core_55_1j',
+'sorAra1' => 'sorex_araneus_core_55_1e',
+'speTri1' => 'spermophilus_tridecemlineatus_core_55_1g',
+'taeGut1' => 'taeniopygia_guttata_core_55_1b',
+'fr2' => 'takifugu_rubripes_core_55_4k',
+'tarSyr1' => 'tarsius_syrichta_core_55_1c',
+'tetNig2' => 'tetraodon_nigroviridis_core_55_8b',
+'tupBel1' => 'tupaia_belangeri_core_55_1f',
+'turTru1' => 'tursiops_truncatus_core_55_1c',
+'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 @ensGtfReference;
+$ensGtfReference[55] = \%ensGeneGtfFileNames_55;
$ensGtfReference[52] = \%ensGeneGtfFileNames_52;
$ensGtfReference[51] = \%ensGeneGtfFileNames_51;
$ensGtfReference[50] = \%ensGeneGtfFileNames_50;
$ensGtfReference[49] = \%ensGeneGtfFileNames_49;
@@ -888,8 +1053,9 @@
$ensGtfReference[47] = \%ensGeneGtfFileNames_47;
$ensGtfReference[46] = \%ensGeneGtfFileNames_46;
$ensGtfReference[35] = \%ensGeneGtfFileNames_35;
my @ensPepReference;
+$ensPepReference[55] = \%ensGeneFtpPeptideFileNames_55;
$ensPepReference[52] = \%ensGeneFtpPeptideFileNames_52;
$ensPepReference[51] = \%ensGeneFtpPeptideFileNames_51;
$ensPepReference[50] = \%ensGeneFtpPeptideFileNames_50;
$ensPepReference[49] = \%ensGeneFtpPeptideFileNames_49;
@@ -897,8 +1063,9 @@
$ensPepReference[47] = \%ensGeneFtpPeptideFileNames_47;
$ensPepReference[46] = \%ensGeneFtpPeptideFileNames_46;
$ensPepReference[35] = \%ensGeneFtpPeptideFileNames_35;
my @ensMySqlReference;
+$ensMySqlReference[55] = \%ensGeneFtpMySqlFileNames_55;
$ensMySqlReference[52] = \%ensGeneFtpMySqlFileNames_52;
$ensMySqlReference[51] = \%ensGeneFtpMySqlFileNames_51;
$ensMySqlReference[50] = \%ensGeneFtpMySqlFileNames_50;
$ensMySqlReference[49] = \%ensGeneFtpMySqlFileNames_49;