diff --git a/bioframe/io/data/_assemblies.yml b/bioframe/io/data/_assemblies.yml index 8ae3c7e9..e44eda74 100644 --- a/bioframe/io/data/_assemblies.yml +++ b/bioframe/io/data/_assemblies.yml @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -99,7 +99,7 @@ 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 @@ -107,7 +107,7 @@ 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 @@ -115,7 +115,7 @@ 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 @@ -123,7 +123,7 @@ 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 @@ -131,7 +131,7 @@ 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 @@ -139,7 +139,7 @@ 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 @@ -147,7 +147,7 @@ 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 @@ -155,4 +155,4 @@ 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/ diff --git a/docs/guide-io.ipynb b/docs/guide-io.ipynb index 2ae7f3cb..eeae7146 100644 --- a/docs/guide-io.ipynb +++ b/docs/guide-io.ipynb @@ -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", diff --git a/docs/tutorials/tutorial_assign_peaks_to_genes.ipynb b/docs/tutorials/tutorial_assign_peaks_to_genes.ipynb index 58720ef8..86d5b5de 100644 --- a/docs/tutorials/tutorial_assign_peaks_to_genes.ipynb +++ b/docs/tutorials/tutorial_assign_peaks_to_genes.ipynb @@ -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",