Update hgdownload url in docs

open2c · Feb 8, 2024 · 2f0a852 · 2f0a852
1 parent 37ffae6
commit 2f0a852
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Showing 3 changed files with 15 additions and 15 deletions.
diff --git 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
@@ -99,60 +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/
diff --git 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
@@ -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",