09-tutorial.ipynb

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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Intermine-Python: Tutorial 9: Creating Lists"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This tutorial will talk about how you can create and save lists in your account. Like the previous tutorial, you will need to provide your login information while creating a service object. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "You can either provide a list of identifiers (for example, gene symbols) and the Intermine Server will try to resolve them into objects in the database or you provide a query that specifies exactly what you want. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from intermine.webservice import Service"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Enter your login information, uncomment the line of code and then run it. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "service=Service(\"https://www.flymine.org/flymine/service\",username=\"demo@intermine.org\",password=\"demo\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We will look at three methods in this tutorial. Let's say you want to upload a list of strings (Gene Symbols). We begin by declaring a list, which I've called symbols. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "symbols=[\"eve\",\"zen\",\"rudimentary\"]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Note that you can use their secondary identifiers or DB identifiers instead if you're more comfortable with that. So if you changed symbols to [\"CG2328\",\"zen\",\"rudimentary\"] or [\"eve\",\"FBgn0004053\",\"rudimentary] it would not be an issue as Intermine would be able to resolve it for you. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To create a list, you need to declare a list manager object. We then use the create_list method as shown below. Remember to define a name for the list, otherwise the list will be lost once the session will be terminated. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "lm=service.list_manager()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<intermine.lists.list.List at 0x7f28805744a8>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lm.delete_lists([\"my list\"])\n",
    "lm.create_list(content=symbols,list_type=\"Gene\",name=\"my list\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We will now look at how you can save a list from a query. Suppose that you want to extract only the information regarding the gene symbol \"eve\" stored in the previous list that we uploaded. You can do it as shown below. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "query=service.new_query(\"Gene\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<ListConstraint: Gene IN my list>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "query.add_constraint(\"Gene\",\"IN\",\"my list\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<BinaryConstraint: Gene.symbol = eve>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "query.add_constraint(\"symbol\",\"=\",\"eve\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<intermine.lists.list.List at 0x7f28804c63c8>"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lm.delete_lists([\"my list 2\"])\n",
    "lm.create_list(query,name=\"my list 2\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Finally, let's say that you have a file with a list of gene identifiers stored on your machine, which you want to upload as a list. Change the string stored to match the path location of your file. Uncomment the lines of code and run it. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "#file=\"Enter/File/Path.tsv\"\n",
    "#lm.create_list(file,list_type=\"Gene\",name=\"my list 3\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If you want to view the names of all the lists available, use the following:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "dict_keys(['Gene List (Fri Aug 23 2019 15:39:10 GMT+0100 (British Summer Time))', 'Gene List (Mon Jun 03 2019 14:12:11 GMT+0100 (BST))', 'Gene list for D. melanogaster 03 Jun 2019 13:10:42', 'H. sapiens orthologues of FlyTF_site_specific_1', 'PL FlyAtlas_brain_top', 'PL FlyAtlas_head_top', 'PL FlyAtlas_hindgut_top', 'PL FlyAtlas_maleglands_top', 'PL FlyAtlas_ovary_top', 'PL FlyAtlas_testis_top', 'PL FlyAtlas_tubules_top', 'PL FlyTF_PWM_TFs', 'PL FlyTF_REDfly_TFs', 'PL FlyTF_putativeTFs', 'PL FlyTF_site_specific_TFs', 'PL FlyTF_trusted_TFs', 'PL classI', 'PL classII', 'PL classIII', 'PL classIIIa', 'PL classIIIb', 'PL classIIIc', 'PL classIIa', 'PL classIIb', 'PL classIIc', 'PL classIa', 'PL classIb', 'PL dme_immunity_genes', 'Testing stuff', 'UseCase1_transcripts_ERstress', 'UseCase1_transcripts_oxidativeStress', 'UseCase5_ScreenHits', 'UseCase5_backgroundGeneList', 'bobo', 'bobo_1', 'combination-1', 'combination-2', 'esyN demo list', 'esyN demo list_1', 'my list', 'my list 2', 'my_list_1'])"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "lm.get_all_list_names()"
   ]
  }
 ],
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