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      "source": "# Linking endpoints together\n\nIf you can pull a datapoint from the json, you can use it as input for another endpoint.\n\nFor example, this script gets the genomic locus of a gene then looks up repeats overlapping it:"
    },
    {
      "metadata": {
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      "cell_type": "code",
      "source": "library(httr)\nlibrary(jsonlite)\n\nfetch_endpoint <- function(server, request, content_type){\n\n    r <- GET(paste(server, request, sep = \"\"), accept(content_type))\n\n    stop_for_status(r)\n\n    if (content_type == 'application/json'){\n        return (fromJSON(content(r, \"text\", encoding = \"UTF-8\")))\n    } else {\n        return (content(r, \"text\", encoding = \"UTF-8\"))\n    }\n}\n\nserver <- \"http://rest.ensembl.org/\"\ngene_ext <- \"lookup/id/TraesCS3D02G007500?\"\njson <- \"application/json\"\nget_gene <- fetch_endpoint(server, gene_ext, json)\n\nlocus = paste(get_gene$species, \"/\", get_gene$seq_region_name, \":\",get_gene$start, \"..\", get_gene$end, sep=\"\")\n\next_get_bed <- paste(\"overlap/region/\", locus, \"?feature=repeat\", sep = \"\")\n\nget_bed <- fetch_endpoint(server, ext_get_bed, \"text/x-bed\")\n\n# print the bed file\ncat(get_bed)",
      "execution_count": null,
      "outputs": []
    },
    {
      "metadata": {},
      "cell_type": "markdown",
      "source": "## Exercises 5\n\n1\\. Using the script from 3.1, add a call to fetch and print the sequence for the gene BCH1 in FASTA format."
    },
    {
      "metadata": {
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      "cell_type": "code",
      "source": "# Exercise 5.1",
      "execution_count": null,
      "outputs": []
    },
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      "metadata": {},
      "cell_type": "markdown",
      "source": "2\\. Print the ID of any variants that overlap the region 5000 bp upstream of the Brachypodium BRADI_5g16840v3 gene. (Hints: get the gene ID first, then check the strand of the gene to see which way is upstream.)"
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "# Exercise 5.2",
      "execution_count": null,
      "outputs": []
    },
    {
      "metadata": {},
      "cell_type": "markdown",
      "source": "[Next page: Exercises 5 - answers](5_Linking_endpoints_together_answers.ipynb)"
    }
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