{
  "cells": [
    {
      "metadata": {
        "collapsed": true
      },
      "cell_type": "markdown",
      "source": "## Exercises 4 – answers \n\n1\\. Get the gene tree predicted for the gene ENSG00000189221 in full nh format. "
    },
    {
      "metadata": {
        "trusted": true
      },
      "cell_type": "code",
      "source": "library(httr)\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\ngene_id <- \"ENSG00000189221\"\n\n# define the general URL parameters\nserver <- \"http://rest.ensembl.org/\"\next_gt <- paste(\"genetree/member/id/\", gene_id, \"?nh_format=full;\", sep = \"\")\ngt_content_type <- \"text/x-nh\"\nget_gt <- fetch_endpoint(server, ext_gt, gt_content_type)\n\ncat(get_gt)",
      "execution_count": null,
      "outputs": []
    },
    {
      "metadata": {},
      "cell_type": "markdown",
      "source": "2\\. Get the sequence of the gene ENSG00000157764 in FASTA."
    },
    {
      "metadata": {
        "trusted": true
      },
      "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\ngene <- \"ENSG00000157764\"\nserver <- \"http://rest.ensembl.org/\"\next_get_seq <- paste(\"/sequence/id/\", gene, \"?\", sep = \"\")\ncon <- \"text/x-fasta\"\n\nget_seq <- fetch_endpoint(server, ext_get_seq, con)\n\n# print the gene name, ID and sequence\ncat(get_seq)",
      "execution_count": null,
      "outputs": []
    },
    {
      "metadata": {},
      "cell_type": "markdown",
      "source": "[Next page: Linking endpoints together](5_Linking_endpoints_together.ipynb)"
    }
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