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Commit 1bbe83c2 authored by Monika Komorowska's avatar Monika Komorowska
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replaced parameter dependent with dependent_on to resolve the ambiguity

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misc-scripts/xref_mapping/xref_config.ini
+ 54
− 58
View file @ 1bbe83c2
# $Id$
########################################################################
# SOURCES #
# #
# Keys: #
# name - name of this source (required) #
# download - must be downloaded (Y or N, required) #
# order - parsing order for this source #
# priority - priority of these data files when more files belong #
# to the same source 'name' #
# prio_descr - label for the 'priority' #
# parser - the parser to be used (required) #
# release_uri - URI pointing to release information (optional) #
# data_uri - URI pointing to the data files (multiple, required) #
# dependent - These must be loaded first #
# Note is sepecies does not have this source then test #
# ignores these #
# #
########################################################################
##########################################################################
# SOURCES #
# #
# Keys: #
# name - name of this source (required) #
# download - must be downloaded (Y or N, required) #
# order - parsing order for this source #
# priority - priority of these data files when more files belong #
# to the same source 'name' #
# prio_descr - label for the 'priority' #
# parser - the parser to be used (required) #
# release_uri - URI pointing to release information (optional) #
# data_uri - URI pointing to the data files (multiple, required) #
# dependent_on - Comma separated list of sources which must be loaded #
# first. #
# Note that if species does not have xrefs from a #
# master source specified in this list than the #
# dependency is ignored #
# #
##########################################################################
[source EC_NUMBER::saccharomyces_cerevisiae]
# Used by S.cerevisiae
......@@ -202,7 +204,7 @@ order = 50
priority = 1
prio_descr =
parser = PHIbaseParser
dependent = Uniprot/SWISSPROT,Uniprot/SPTREMBL
dependent_on = Uniprot/SWISSPROT,Uniprot/SPTREMBL
release_uri =
data_uri = http://www.phi-base.org/PHI-export.php
......@@ -597,7 +599,7 @@ order = 100
priority = 1
prio_descr =
parser = FantomParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT
release_uri =
data_uri = ftp://fantom.gsc.riken.jp/FANTOM3/DDBJ/DDBJ_fantom3_HTC_accession.txt.gz
......@@ -620,7 +622,7 @@ order = 100
priority = 1
prio_descr = ID assigned by FlyBase
parser = FlybaseParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri =
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/gff/dmel-all-*.gff.gz
......@@ -632,7 +634,7 @@ order = 100
priority = 1
prio_descr = ID assigned by FlyBase
parser = FlybaseParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri =
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-*.gff.gz
......@@ -644,7 +646,7 @@ order = 100
priority = 1
prio_descr = ID assigned by FlyBase
parser = FlybaseParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri =
data_uri = ftp://ftp.flybase.org/releases/current/dgri_r1.3/gff/dgri-all-r1.3.gff.gz
......@@ -656,7 +658,7 @@ order = 100
priority = 1
prio_descr = ID assigned by FlyBase
parser = FlybaseParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri =
data_uri = ftp://ftp.flybase.org/releases/current/dwil_r1.3/gff/dwil-all-r1.3.gff.gz
......@@ -668,7 +670,7 @@ order = 100
priority = 1
prio_descr = ID assigned by FlyBase
parser = FlybaseParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri =
data_uri = ftp://ftp.flybase.org/releases/current/dana_r1.3/gff/dana-all-r1.3.gff.gz
......@@ -680,7 +682,7 @@ order = 100
priority = 1
prio_descr = ID assigned by FlyBase
parser = FlybaseParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri =
data_uri = ftp://ftp.flybase.org/releases/current/dyak_r1.3/gff/dyak-all-r1.3.gff.gz
......@@ -692,7 +694,7 @@ order = 100
priority = 1
prio_descr = ID assigned by FlyBase
parser = FlybaseParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri =
data_uri = ftp://ftp.flybase.org/releases/current/dsim_r1.3/gff/dsim-all-r1.3.gff.gz
......@@ -704,7 +706,7 @@ order = 100
priority = 1
prio_descr = ID assigned by FlyBase
parser = FlybaseParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri =
data_uri = ftp://ftp.flybase.org/releases/current/dsec_r1.3/gff/dsec-all-r1.3.gff.gz
......@@ -717,7 +719,7 @@ order = 100
priority = 1
prio_descr = ID assigned by FlyBase
parser = FlybaseParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri =
data_uri = ftp://ftp.flybase.org/releases/current/dere_r1.3/gff/dere-all-r1.3.gff.gz
......@@ -729,7 +731,7 @@ order = 100
priority = 1
prio_descr = ID assigned by FlyBase
parser = FlybaseParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri =
data_uri = ftp://ftp.flybase.org/releases/current/dper_r1.3/gff/dper-all-r1.3.gff.gz
......@@ -741,7 +743,7 @@ order = 100
priority = 1
prio_descr = ID assigned by FlyBase
parser = FlybaseParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri =
data_uri = ftp://ftp.flybase.org/releases/current/dmoj_r1.3/gff/dmoj-all-r1.3.gff.gz
......@@ -753,7 +755,7 @@ order = 100
priority = 1
prio_descr = ID assigned by FlyBase
parser = FlybaseParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro
release_uri =
data_uri = ftp://ftp.flybase.org/releases/current/dvir_r1.2/gff/dvir-all-r1.2.gff.gz
......@@ -952,7 +954,7 @@ order = 80
priority = 1
prio_descr = main
parser = GOParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide,SGD
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide,SGD
release_uri = http://www.ebi.ac.uk/GOA/uniprot_release.html
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz
data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz
......@@ -965,7 +967,7 @@ order = 85
priority = 2
prio_descr = interpro
parser = InterproGoParser
dependent = GO
dependent_on = GO
release_uri =
data_uri = http://www.geneontology.org/external2go/interpro2go
......@@ -977,7 +979,7 @@ order = 85
priority = 1
prio_descr = main
parser = GOParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide,wormbase_all
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide,wormbase_all
release_uri =
data_uri = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.wb.gz
......@@ -990,13 +992,11 @@ order = 85
priority = 1
prio_descr = main
parser = Use by GOParser
dependent =
dependent_on =
release_uri =
data_uri =
[source GO::danio_rerio]
# Used by danio_rerio
name = GO
......@@ -1005,7 +1005,7 @@ order = 85
priority = 1
prio_descr = main
parser = GOParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
release_uri =
data_uri = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.zfin.gz
data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz
......@@ -1018,7 +1018,7 @@ order = 120
priority = 1
prio_descr = main
parser = GOSlimParser
dependent = GO
dependent_on = GO
release_uri =
#data_uri = script:
data_uri = script:host=>ens-staging1,dbname=>ensembl_ontology_67,
......@@ -1031,7 +1031,7 @@ order = 120
priority = 1
prio_descr = main
parser = GOSlimParser
dependent = GO
dependent_on = GO
release_uri =
data_uri = script:host=>mysql-eg-pan-1.ebi.ac.uk,port=>4276,dbname=>ensemblgenomes_ontology_14_67,
......@@ -1043,7 +1043,7 @@ order = 85
priority = 1
prio_descr = main
parser = GOParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
release_uri = http://www.ebi.ac.uk/GOA/HUMAN_release.html
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz
data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz
......@@ -1056,7 +1056,7 @@ order = 85
priority = 1
prio_descr = main
parser = GOParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
release_uri = http://www.ebi.ac.uk/GOA/MOUSE_release.html
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/MOUSE/gene_association.goa_mouse.gz
data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz
......@@ -1070,7 +1070,7 @@ data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.
# priority = 1
# prio_descr = goga
# parser = GOParser
# dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
# dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
# release_uri =
# data_uri = http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.mgi.gz
# data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz
......@@ -1083,7 +1083,7 @@ order = 85
priority = 1
prio_descr = main
parser = GOParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
release_uri = http://www.ebi.ac.uk/GOA/rat_release.html
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/RAT/gene_association.goa_rat.gz
data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz
......@@ -1096,7 +1096,7 @@ order = 85
priority = 1
prio_descr = main
parser = GOParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide,SGD
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide,SGD
release_uri =
data_uri = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.sgd.gz
data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz
......@@ -1121,7 +1121,7 @@ order = 85
priority = 2
prio_descr = goga
parser = GOParser
dependent = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
release_uri =
data_uri = http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.fb.gz
data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz
......@@ -1201,7 +1201,7 @@ order = 29
priority = 4
prio_descr = entrezgene_manual
parser = HGNCParser
dependent = EntrezGene,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
dependent_on = EntrezGene,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
release_uri =
data_uri = http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Genew+output+data&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_refseq_ids&col=md_eg_id&col=md_refseq_id&col=gd_pub_ensembl_id&col=md_prot_id&col=gd_lsdb_links&status=Approved&status=Approved+Non-Human&status_opt=3&=on&where=&order_by=gd_hgnc_id&limit=&format=text&submit=submit&.cgifields=&.cgifields=status&.cgifields=chr
......@@ -1490,7 +1490,7 @@ order = 60
priority = 1
prio_descr =
parser = Mim2GeneParser
dependent = MIM,EntrezGene
dependent_on = MIM,EntrezGene
release_uri =
data_uri = ftp://grcf.jhmi.edu/OMIM/mim2gene.txt
......@@ -1559,7 +1559,7 @@ order = 50
priority = 1
prio_descr =
parser = OrphanetParser
dependent = HGNC
dependent_on = HGNC
release_uri =
data_uri = http://www.orphadata.org/data/xml/en_product6.xml
......@@ -1600,7 +1600,7 @@ order = 30
priority = 1
prio_descr =
parser = RGDParser
dependent = RefSeq_dna,RefSeq_peptide
dependent_on = RefSeq_dna,RefSeq_peptide
release_uri =
data_uri = ftp://rgd.mcw.edu/pub/data_release/GENES_RAT.txt
......@@ -1677,7 +1677,6 @@ order = 20
priority = 1
prio_descr = refseq
parser = RefSeqParser
dependent = RefSeq_dna
release_uri =
[source RefSeq_mRNA::CCDS]
......@@ -1698,7 +1697,6 @@ order = 20
priority = 1
prio_descr =
parser = RefSeqParser
dependent = RefSeq_dna
release_uri =
[source RefSeq_mRNA_predicted::MULTI]
......@@ -1709,7 +1707,6 @@ order = 20
priority = 1
prio_descr = refseq
parser = RefSeqParser
dependent = RefSeq_dna
release_uri =
[source RefSeq_mRNA_predicted::CCDS]
......@@ -1730,7 +1727,6 @@ order = 20
priority = 1
prio_descr =
parser = RefSeqParser
dependent = RefSeq_dna
release_uri =
[source RefSeq_dna::MULTI-vertebrate_mammalian]
......@@ -2748,7 +2744,7 @@ order = 20
priority = 1
prio_descr =
parser = UniProtAltParser
dependent = MIM
dependent_on = MIM
release_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/reldate.txt
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz
......@@ -2783,7 +2779,7 @@ order = 20
priority = 2
prio_descr = sequence_mapped
parser = UniProtAltParser
dependent = MIM
dependent_on = MIM
release_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/reldate.txt
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz
......@@ -2802,7 +2798,7 @@ order = 22
priority = 1
prio_descr = uniprot_mapped
parser = UniProtDirectParser
dependent = Unprot/SWISSPROT
dependent_on = Unprot/SWISSPROT
release_uri =
data_uri = script:wget=>ftp://ftp.ebi.ac.uk/pub/contrib/xrefs/ens-sp.map,host=>ens-staging1,dbname=>ensembl_production,
......
misc-scripts/xref_mapping/xref_config2sql.pl
+ 2
− 11
View file @ 1bbe83c2
......@@ -113,7 +113,7 @@ foreach my $source_section ( sort( $config->GroupMembers('source') ) ) {
print("\n");
my @dependents =
split( /\,/, $config->val( $source_section, 'dependent', '' ) );
split( /\,/, $config->val( $source_section, 'dependent_on', '' ) );
foreach my $dep (@dependents){
print "# adding source dependency that $source_section needs $dep loaded first\n";
......@@ -188,16 +188,7 @@ foreach my $species_section ( sort( $config->GroupMembers('species') ) )
print("\n");
my @dependents =
split( /\,/, $config->val( $source_section, 'dependent', '' ) );
foreach my $dep (@dependents){
print "# adding source dependency that $source_section needs $dep loaded first\n";
print "INSERT IGNORE INTO dependent_source (master_source_id, dependent_name)\n";
printf( "VALUES (%d, '%s');\n\n", $source_ids{$source_section}, $dep);
}
} ## end foreach my $source_name ( sort...)
} ## end foreach my $species_section...
print "# FINISEHD SUCCESSFULLY\n"
print "# FINISHED SUCCESSFULLY\n"
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