remove custom org dbs from annotation table

Author: torres-alexis

GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv

@@ -1,23 +1,23 @@
 name,species,strain,ensemblVersion,ref_source,fasta,gtf,taxon,annotations,genelab_annots_link,genelab_annots_info_link
 ARABIDOPSIS,Arabidopsis thaliana,,59,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.59.gtf.gz,3702,org.At.tair.db,https://figshare.com/ndownloader/files/48354355,https://figshare.com/ndownloader/files/48354352
-BACSU,Bacillus subtilis,subsp. subtilis 168,59,ensembl_bacteria,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/fasta/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/dna/Bacillus_subtilis_subsp_subtilis_str_168_gca_000009045.ASM904v1.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/gtf/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/Bacillus_subtilis_subsp_subtilis_str_168_gca_000009045.ASM904v1.59.gtf.gz,224308,org.Bsubtilissubspsubtilis168.eg.db,https://figshare.com/ndownloader/files/48354346,https://figshare.com/ndownloader/files/48354349
-BRADI,Brachypodium distachyon,,59,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/fasta/brachypodium_distachyon/dna/Brachypodium_distachyon.Brachypodium_distachyon_v3.0.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/gtf/brachypodium_distachyon/Brachypodium_distachyon.Brachypodium_distachyon_v3.0.59.gtf.gz,15368,org.Bdistachyon.eg.db,https://figshare.com/ndownloader/files/48354370,https://figshare.com/ndownloader/files/48354361
+BACSU,Bacillus subtilis,subsp. subtilis 168,59,ensembl_bacteria,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/fasta/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/dna/Bacillus_subtilis_subsp_subtilis_str_168_gca_000009045.ASM904v1.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/gtf/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/Bacillus_subtilis_subsp_subtilis_str_168_gca_000009045.ASM904v1.59.gtf.gz,224308,,https://figshare.com/ndownloader/files/48354346,https://figshare.com/ndownloader/files/48354349
+BRADI,Brachypodium distachyon,,59,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/fasta/brachypodium_distachyon/dna/Brachypodium_distachyon.Brachypodium_distachyon_v3.0.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/gtf/brachypodium_distachyon/Brachypodium_distachyon.Brachypodium_distachyon_v3.0.59.gtf.gz,15368,,https://figshare.com/ndownloader/files/48354370,https://figshare.com/ndownloader/files/48354361
 BRARP,Brassica rapa,,59,ensembl_plants,http://ftp.ensemblgenomes.org/pub/plants/release-59/fasta/brassica_rapa/dna/Brassica_rapa.Brapa_1.0.dna.toplevel.fa.gz,http://ftp.ensemblgenomes.org/pub/plants/release-59/gtf/brassica_rapa/Brassica_rapa.Brapa_1.0.59.gtf.gz,,,,
 WORM,Caenorhabditis elegans,,112,ensembl,https://ftp.ensembl.org/pub/release-112/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz,https://ftp.ensembl.org/pub/release-112/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.112.gtf.gz,6239,org.Ce.eg.db,https://figshare.com/ndownloader/files/48354373,https://figshare.com/ndownloader/files/48354364
 ZEBRAFISH,Danio rerio,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.primary_assembly.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/danio_rerio/Danio_rerio.GRCz11.112.gtf.gz,7955,org.Dr.eg.db,https://figshare.com/ndownloader/files/48354388,https://figshare.com/ndownloader/files/48354367
 FLY,Drosophila melanogaster,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.46.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.46.112.gtf.gz,7227,org.Dm.eg.db,https://figshare.com/ndownloader/files/48354382,https://figshare.com/ndownloader/files/48354376
 ERCC,,,,ThermoFisher,https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip,https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip,,,,
-ECOLI,Escherichia coli,str. K-12 substr. MG1655,59,ensembl_bacteria,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/fasta/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655_gca_000005845/dna/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/gtf/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655_gca_000005845/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.59.gtf.gz,511145,org.EcolistrK12substrMG1655.eg.db,https://figshare.com/ndownloader/files/48354379,https://figshare.com/ndownloader/files/48354394
+ECOLI,Escherichia coli,str. K-12 substr. MG1655,59,ensembl_bacteria,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/fasta/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655_gca_000005845/dna/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-59/gtf/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655_gca_000005845/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.59.gtf.gz,511145,,https://figshare.com/ndownloader/files/48354379,https://figshare.com/ndownloader/files/48354394
 HUMAN,Homo sapiens,,112,ensembl,https://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz,https://ftp.ensembl.org/pub/release-112/gtf/homo_sapiens/Homo_sapiens.GRCh38.112.gtf.gz,9606,org.Hs.eg.db,https://figshare.com/ndownloader/files/48354445,https://figshare.com/ndownloader/files/48354448
 ,Lactobacillus acidophilus,NCFM,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/985/GCF_000011985.1_ASM1198v1/GCF_000011985.1_ASM1198v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/985/GCF_000011985.1_ASM1198v1/GCF_000011985.1_ASM1198v1_genomic.gtf.gz,272621,,https://figshare.com/ndownloader/files/49061254,https://figshare.com/ndownloader/files/49061257
 MOUSE,Mus musculus,,112,ensembl,https://ftp.ensembl.org/pub/release-112/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz,https://ftp.ensembl.org/pub/release-112/gtf/mus_musculus/Mus_musculus.GRCm39.112.gtf.gz,10090,org.Mm.eg.db,https://figshare.com/ndownloader/files/48354460,https://figshare.com/ndownloader/files/48354457
 ,Mycobacterium marinum,M,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/018/345/GCF_000018345.1_ASM1834v1/GCF_000018345.1_ASM1834v1_genomic.gtf.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/018/345/GCF_000018345.1_ASM1834v1/GCF_000018345.1_ASM1834v1_genomic.gtf.gz,216594,,https://figshare.com/ndownloader/files/49061260,https://figshare.com/ndownloader/files/49061263
 ORYSJ,Oryza sativa,Japonica,59,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/fasta/oryza_sativa/dna/Oryza_sativa.IRGSP-1.0.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/gtf/oryza_sativa/Oryza_sativa.IRGSP-1.0.59.gtf.gz,39947,,https://figshare.com/ndownloader/files/48354451,https://figshare.com/ndownloader/files/48354454
-ORYLA,Oryzias latipes,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/oryzias_latipes/dna/Oryzias_latipes.ASM223467v1.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/oryzias_latipes/Oryzias_latipes.ASM223467v1.112.gtf.gz,8090,org.Olatipes.eg.db,https://figshare.com/ndownloader/files/48354463,https://figshare.com/ndownloader/files/48354466
+ORYLA,Oryzias latipes,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/oryzias_latipes/dna/Oryzias_latipes.ASM223467v1.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/oryzias_latipes/Oryzias_latipes.ASM223467v1.112.gtf.gz,8090,,https://figshare.com/ndownloader/files/48354463,https://figshare.com/ndownloader/files/48354466
 ,Pseudomonas aeruginosa,UCBPP-PA14,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/014/625/GCF_000014625.1_ASM1462v1/GCF_000014625.1_ASM1462v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/014/625/GCF_000014625.1_ASM1462v1/GCF_000014625.1_ASM1462v1_genomic.gtf.gz,208963,,https://figshare.com/ndownloader/files/49061266,https://figshare.com/ndownloader/files/49061269
 RAT,Rattus norvegicus,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/rattus_norvegicus/dna/Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/rattus_norvegicus/Rattus_norvegicus.mRatBN7.2.112.gtf.gz,10116,org.Rn.eg.db,https://figshare.com/ndownloader/files/48354472,https://figshare.com/ndownloader/files/48354475
 YEAST,Saccharomyces cerevisiae,S288C,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.112.gtf.gz,559292,org.Sc.sgd.db,https://figshare.com/ndownloader/files/48354469,https://figshare.com/ndownloader/files/48354478
-SALTY,Salmonella enterica,serovar Typhimurium str. LT2,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/945/GCF_000006945.2_ASM694v2/GCF_000006945.2_ASM694v2_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/945/GCF_000006945.2_ASM694v2/GCF_000006945.2_ASM694v2_genomic.gtf.gz,99287,org.SentericaserovarTyphimuriumstrLT2.eg.db,https://figshare.com/ndownloader/files/49061272,https://figshare.com/ndownloader/files/49061275
+SALTY,Salmonella enterica,serovar Typhimurium str. LT2,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/945/GCF_000006945.2_ASM694v2/GCF_000006945.2_ASM694v2_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/945/GCF_000006945.2_ASM694v2/GCF_000006945.2_ASM694v2_genomic.gtf.gz,99287,,https://figshare.com/ndownloader/files/49061272,https://figshare.com/ndownloader/files/49061275
 ,Serratia liquefaciens,ATCC 27592,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/422/085/GCF_000422085.1_ASM42208v1/GCF_000422085.1_ASM42208v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/422/085/GCF_000422085.1_ASM42208v1/GCF_000422085.1_ASM42208v1_genomic.gtf.gz,1346614,,https://figshare.com/ndownloader/files/49061278,https://figshare.com/ndownloader/files/49061281
 ,Staphylococcus aureus,MRSA252,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/505/GCF_000011505.1_ASM1150v1/GCF_000011505.1_ASM1150v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/505/GCF_000011505.1_ASM1150v1/GCF_000011505.1_ASM1150v1_genomic.gtf.gz,282458,,https://figshare.com/ndownloader/files/49061284,https://figshare.com/ndownloader/files/49061287
 ,Streptococcus mutans,UA159,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/007/465/GCF_000007465.2_ASM746v2/GCF_000007465.2_ASM746v2_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/007/465/GCF_000007465.2_ASM746v2/GCF_000007465.2_ASM746v2_genomic.gtf.gz,210007,,https://figshare.com/ndownloader/files/49061290,https://figshare.com/ndownloader/files/49061293