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Update hgdownload url in docs and assembly info #187

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Feb 8, 2024
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Update hgdownload url in docs and assembly info #187

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26 changes: 13 additions & 13 deletions bioframe/io/data/_assemblies.yml
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Expand Up @@ -15,7 +15,7 @@
cytobands: hg19.cytoband.tsv
default_roles: [assembled]
default_units: [primary, non-nuclear]
url: https://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/
url: https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/
- organism: homo sapiens
provider: ncbi
provider_build: GRCh38
Expand All @@ -33,7 +33,7 @@
cytobands: hg38.cytoband.tsv
default_roles: [assembled]
default_units: [primary, non-nuclear]
url: https://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/
url: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/
- organism: homo sapiens
provider: ncbi
provider_build: T2T-CHM13v2.0
Expand All @@ -51,7 +51,7 @@
cytobands: hs1.cytoband.tsv
default_roles: [assembled]
default_units: [primary, non-nuclear]
url: https://hgdownload.cse.ucsc.edu/goldenPath/hs1/bigZips/
url: https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/
- organism: mus musculus
provider: ncbi
provider_build: MGSCv37
Expand All @@ -67,7 +67,7 @@
seqinfo: mm9.seqinfo.tsv
default_roles: [assembled]
default_units: [primary, non-nuclear]
url: https://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/
url: https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/
- organism: mus musculus
provider: ncbi
provider_build: GRCm38
Expand All @@ -83,7 +83,7 @@
seqinfo: mm10.seqinfo.tsv
default_roles: [assembled]
default_units: [primary, non-nuclear]
url: https://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/
url: https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/
- organism: mus musculus
provider: ncbi
provider_build: GRCm39
Expand All @@ -99,60 +99,60 @@
seqinfo: mm39.seqinfo.tsv
default_roles: [assembled]
default_units: [primary, non-nuclear]
url: https://hgdownload.cse.ucsc.edu/goldenPath/mm39/bigZips/
url: https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/
- organism: drosophila melanogaster
provider: ucsc
provider_build: dm3
release_year: 2006
seqinfo: dm3.seqinfo.tsv
default_roles: [assembled]
default_units: [primary, non-nuclear]
url: https://hgdownload.cse.ucsc.edu/goldenPath/dm3/bigZips/
url: https://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/
- organism: drosophila melanogaster
provider: ucsc
provider_build: dm6
release_year: 2014
seqinfo: dm6.seqinfo.tsv
default_roles: [assembled]
default_units: [primary, non-nuclear]
url: https://hgdownload.cse.ucsc.edu/goldenPath/dm6/bigZips/
url: https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/
- organism: caenorhabditis elegans
provider: ucsc
provider_build: ce10
release_year: 2010
seqinfo: ce10.seqinfo.tsv
default_roles: [assembled]
default_units: [primary, non-nuclear]
url: https://hgdownload.cse.ucsc.edu/goldenPath/ce10/bigZips/
url: https://hgdownload.soe.ucsc.edu/goldenPath/ce10/bigZips/
- organism: caenorhabditis elegans
provider: ucsc
provider_build: ce11
release_year: 2013
seqinfo: ce11.seqinfo.tsv
default_roles: [assembled]
default_units: [primary, non-nuclear]
url: https://hgdownload.cse.ucsc.edu/goldenPath/ce11/bigZips/
url: https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/
- organism: danio rerio
provider: ucsc
provider_build: danRer10
release_year: 2014
seqinfo: danRer10.seqinfo.tsv
default_roles: [assembled]
default_units: [primary, non-nuclear]
url: https://hgdownload.cse.ucsc.edu/goldenPath/danRer10/bigZips/
url: https://hgdownload.soe.ucsc.edu/goldenPath/danRer10/bigZips/
- organism: danio rerio
provider: ucsc
provider_build: danRer11
release_year: 2017
seqinfo: danRer10.seqinfo.tsv
default_roles: [assembled]
default_units: [primary, non-nuclear]
url: https://hgdownload.cse.ucsc.edu/goldenPath/danRer11/bigZips/
url: https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/
- organism: saccharomyces cerevisiae
provider: ucsc
provider_build: sacCer3
release_year: 2011
seqinfo: sacCer3.seqinfo.tsv
default_roles: [assembled]
default_units: [primary, non-nuclear]
url: https://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/bigZips/
url: https://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/
2 changes: 1 addition & 1 deletion docs/guide-io.ipynb
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Expand Up @@ -383,7 +383,7 @@
"> seqinfo: mm9.seqinfo.tsv\n",
"> default_roles: [assembled]\n",
"> default_units: [primary, non-nuclear]\n",
"> url: https://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/\n",
"> url: https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/\n",
"> ...\n",
"> ```\n",
"\n",
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2 changes: 1 addition & 1 deletion docs/tutorials/tutorial_assign_peaks_to_genes.ipynb
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Expand Up @@ -370,7 +370,7 @@
}
],
"source": [
"genes_url = 'https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/genes/hg38.ensGene.gtf.gz'\n",
"genes_url = 'https://hgdownload.soe.ucsc.edu/goldenpath/hg38/bigZips/genes/hg38.ensGene.gtf.gz'\n",
"genes = bioframe.read_table(genes_url, schema='gtf').query('feature==\"CDS\"')\n",
"\n",
"genes.head() \n",
Expand Down
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