From d269e43829c39b7db6211a216c60273c1f3eb93e Mon Sep 17 00:00:00 2001 From: Ian Longden <ianl@sanger.ac.uk> Date: Wed, 12 Nov 2008 17:11:01 +0000 Subject: [PATCH] config changes --- misc-scripts/xref_mapping/xref_config.ini | 143 +++++++++++++++++----- 1 file changed, 111 insertions(+), 32 deletions(-) diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini index 15fec03be5..1228b9068c 100644 --- a/misc-scripts/xref_mapping/xref_config.ini +++ b/misc-scripts/xref_mapping/xref_config.ini @@ -245,7 +245,7 @@ priority = 1 prio_descr = parser = CCDSParser release_uri = -data_uri = script:host=>genebuild4,dbname=>jb16_human_patch_52, +data_uri = script:host=>ens-research,dbname=>ianl_human_ccds_oct08,tran_name=>ENST, [source CCDS::mus_musculus] # Used by mus_musculus @@ -256,7 +256,7 @@ priority = 1 prio_descr = parser = CCDSParser release_uri = -data_uri = script:host=>genebuildx,dbname=>xxx, +data_uri = script:host=>ens-research,dbname=>ianl_mouse_ccds_oct08,tran_name=>ENSMUST, [source Celera_Pep::anopheles_gambiae] # Used by anopheles_gambiae @@ -558,6 +558,7 @@ prio_descr = main parser = GOParser 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/lastest-termdb/go_daily-termdb.obo-xml.gz [source InterproGO::MULTI] # Used by all @@ -591,6 +592,7 @@ prio_descr = main parser = GOParser release_uri = data_uri = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.zfin.gz +data_uri = http://archive.geneontology.org/lastest-termdb/go_daily-termdb.obo-xml.gz [source GO::homo_sapiens] # Used by homo_sapiens @@ -602,6 +604,7 @@ prio_descr = main parser = GOParser 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/lastest-termdb/go_daily-termdb.obo-xml.gz [source GO::mus_musculus] # Used by mus_musculus @@ -613,6 +616,7 @@ prio_descr = main parser = GOParser 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/lastest-termdb/go_daily-termdb.obo-xml.gz [source GO::mus_musculus#01] # Used by mus_musculus @@ -624,6 +628,7 @@ data_uri = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/MOUSE/gene_associatio parser = GOParser release_uri = data_uri = http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.mgi.gz + data_uri = http://archive.geneontology.org/lastest-termdb/go_daily-termdb.obo-xml.gz [source GO::rattus_norvegicus] # Used by rattus_norvegicus @@ -635,6 +640,7 @@ prio_descr = main parser = GOParser 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/lastest-termdb/go_daily-termdb.obo-xml.gz [source HPA::homo_sapiens] @@ -654,11 +660,11 @@ name = HGNC download = Y order = 30 #order 51 -priority = 2 +priority = 1 prio_descr = ccds parser = HGNC_CCDSParser release_uri = -data_uri = script:wget=>http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Genew+output+data&col=gd_hgnc_id&col=gd_pub_refseq_ids&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,dbname=>steve_cdstrack_08may08,host=>genebuild7, +data_uri = script:wget=>http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=HGNC+output+data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_status&col=gd_ccds_ids&status=Approved&status_opt=2&level=pri&=on&where=&order_by=gd_app_sym_sort&limit=&format=text&submit=submit&.cgifields=&.cgifields=level&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag,dbname=>ianl_human_ccds_oct08,host=>ens-research, [source HGNC::homo_sapiens#07] @@ -666,11 +672,11 @@ data_uri = script:wget=>http://www.genenames.org/cgi-bin/hgnc_downloads.c name = HGNC download = N order = 30 -priority = 1 +priority = 2 prio_descr = ensembl_mapped parser = HGNCParser release_uri = -data_uri = file:HGNC/HGNC_TO_ENSG +data_uri = [source HGNC::homo_sapiens] # Used by homo_sapiens @@ -681,7 +687,7 @@ priority = 3 prio_descr = havana parser = HGNC_ENSTParser release_uri = -data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_51_36m, +data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_52_36n, @@ -694,7 +700,7 @@ priority = 4 prio_descr = entrezgene_manual parser = HGNCParser 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=md_ensembl_id&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 +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&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 [source HGNC::homo_sapiens#03] @@ -943,38 +949,81 @@ parser = MIMParser release_uri = data_uri = ftp://ftp.ncbi.nih.gov/repository/OMIM/omim.txt.Z -[source MGI::mus_musculus] +[source MGI::mus_musculus#01] # Used by mus_musculus name = MGI download = N order = 30 -priority = 1 -prio_descr = -parser = MGDParser +priority = 3 +prio_descr = uniprot +parser = release_uri = data_uri = taken from uniprot files +[source MGI::mus_musculus#02] +# Used by mus_musculus +name = MGI +download = Y +order = 45 +priority = 2 +prio_descr = vega +parser = MGI_Vega_Parser +release_uri = +data_uri = script:vhost=>ens-staging,vport=>3306,vdbname=>mus_musculus_vega_52_37e,cdbname=>mus_musculus_core_52_37e,chost=>ens-staging, + +[source MGI::mus_musculus#03] +# Used by mus_musculus +name = MGI +download = Y +order = 1 +priority = 10 +prio_descr = descriptions +parser = MGI_Desc_Parser +release_uri = +data_uri = ftp://ftp.informatics.jax.org/pub/reports/MRK_List2.sql.rpt +data_uri = ftp://ftp.informatics.jax.org/pub/reports/MRK_Synonym.sql.rpt + +[source MGI::mus_musculus#04] +# Used by mus_musculus +name = MGI +download = Y +order = 35 +priority = 1 +prio_descr = ccds +parser = MGI_CCDS_Parser +release_uri = +data_uri = script:wget=>ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_mouse/CCDS.20071128.txt, + + + [source OTTT::homo_sapiens] +# +# NOW taken when merging done with havana +# # Used by homo_sapiens name = OTTT -download = Y +download = N order = 50 priority = 1 prio_descr = parser = OTTTParser release_uri = -data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_51_36m, +data_uri = +#data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_52_36n, [source OTTT::mus_musculus] +# +# NOW taken when merging done with havana +# # Used by mus_musculus name = OTTT -download = Y +download = N order = 50 priority = 1 prio_descr = parser = OTTTParser release_uri = -data_uri = script:host=>ensdb-1-11,port=>5317,dbname=>mus_musculus_vega_51_37d, +data_uri = script:host=>ens-staging,port=>5317,dbname=>mus_musculus_vega_52_37e, [source RGD::rattus_norvegicus] # Used by rattus_norvegicus @@ -1142,7 +1191,7 @@ parser = RefSeqParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz -[source RefSeq_dna::mus_musculus] +[source RefSeq_dna::mus_musculus#01] # Used by mus_musculus name = RefSeq_dna download = Y @@ -1153,6 +1202,18 @@ parser = RefSeqParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/M_musculus/mRNA_Prot/mouse.rna.fna.gz +[source RefSeq_dna::mus_musculus] +# Used by mus_musculus +name = RefSeq_dna +download = Y +order = 25 +priority = 1 +prio_descr = ccds +parser = RefSeq_CCDSParser +release_uri = +data_uri = script:host=>genebuild7,dbname=>steve_cdstrack_08may08, + + [source RefSeq_dna::pan_troglodytes] # Used by pan_troglodytes name = RefSeq_dna @@ -1753,7 +1814,17 @@ priority = 1 prio_descr = parser = HGNC_curated_transcriptParser release_uri = -data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_51_36m, +data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_52_36n, + +[source MGI_curated_transcript::mus_musculus] +name = MGI_curated_transcript +download = Y +order = 49 +priority = 1 +prio_descr = +parser = MGI_curated_transcriptParser +release_uri = +data_uri = script:cdbname=>mus_musculus_core_52_37e,chost=>ens-staging,vhost=>ens-staging,vdbname=>mus_musculus_vega_52_37e, [source Clone_based_vega_transcript::homo_sapiens] @@ -1767,16 +1838,19 @@ release_uri = data_uri = loaded as part of HGNC_curated_transcript -[source Vega_mouse_transcript::mus_musculus] +#[source Vega_mouse_transcript::mus_musculus] # Used by mus_musculus -name = Vega_mouse_transcript -download = Y -order = 50 -priority = 1 -prio_descr = -parser = VegaParser -release_uri = -data_uri = ftp://ftp.sanger.ac.uk/pub/vega/mouse/cdna/Mus_musculus.VEGA.*.cdna.tot.fa.gz +# +# Vega_transcript now used and obtained during merge +# +#name = Vega_mouse_transcript +#download = Y +#order = 50 +#priority = 1 +#prio_descr = +#parser = VegaParser +#release_uri = +#data_uri = ftp://ftp.sanger.ac.uk/pub/vega/mouse/cdna/Mus_musculus.VEGA.*.cdna.tot.fa.gz [source Xenopus_Jamboree::xenopus_tropicalis] # Used by xenopus_tropicalis @@ -2596,9 +2670,9 @@ source = Illumina_V1::homo_sapiens source = Illumina_V2::homo_sapiens source = Interpro::MULTI source = MIM::homo_sapiens -source = OTTT::homo_sapiens +#source = OTTT::homo_sapiens # got from merge source = RefSeq_dna::homo_sapiens -source = RefSeq_dna::homo_sapiens#01 +#source = RefSeq_dna::homo_sapiens#01 source = RefSeq_peptide::homo_sapiens source = UniGene::homo_sapiens source = Uniprot/SPTREMBL::MULTI @@ -2660,15 +2734,20 @@ source = IMGT/GENE_DB::mus_musculus source = IPI::mus_musculus source = Illumina_V1::mus_musculus source = Illumina_V2::mus_musculus +source = MGI::mus_musculus#02 +source = MGI::mus_musculus#03 +source = MGI::mus_musculus#04 +source = MGI_curated_transcript::mus_musculus source = Interpro::MULTI -source = OTTT::mus_musculus +#source = OTTT::mus_musculus # data obtained form merge source = RefSeq_dna::mus_musculus +#source = RefSeq_dna::mus_musculus#01 source = RefSeq_peptide::mus_musculus source = UniGene::mus_musculus source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI -source = Uniprot/Varsplic::MULTI -source = Vega_mouse_transcript::mus_musculus +#source = Uniprot/Varsplic::MULTI +#source = Vega_mouse_transcript::mus_musculus # removed use Vega_transcript source = ncRNA::mus_musculus source = UCSC::mus_musculus -- GitLab