kgml-biopython.ipynb

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  {
   "cell_type": "code",
   "execution_count": 1,
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   },
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   "source": [
    "from see import see"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from Bio.KEGG.REST import *\n",
    "from Bio.KEGG.KGML import KGML_parser"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "pathway = KGML_parser.read(kegg_get(\"ko00061\", \"kgml\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Bio.KEGG.KGML.KGML_pathway.Pathway at 0x103961e10>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pathway"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "     hash()               help()               repr()               str()\n",
       "     .add_entry()         .add_reaction()      .add_relation()      .bounds\n",
       "     .compounds           .element             .entries             .genes\n",
       "     .get_KGML()          .image               .link                .maps\n",
       "     .name                .number              .org                 .orthologs\n",
       "     .reaction_entries    .reactions           .relations\n",
       "     .remove_entry()      .remove_reaction()   .remove_relation()   .title"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "see(pathway)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
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    {
     "name": "stdout",
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     "text": [
      "Help on Pathway in module Bio.KEGG.KGML.KGML_pathway object:\n",
      "\n",
      "class Pathway(__builtin__.object)\n",
      " |  Represents a KGML pathway from KEGG.\n",
      " |  \n",
      " |  Specifies graph information for the pathway map, as described in\n",
      " |  release KGML v0.7.1 (http://www.kegg.jp/kegg/xml/docs/)\n",
      " |  \n",
      " |  Attributes:\n",
      " |  name         KEGGID of the pathway map\n",
      " |  org          ko/ec/[org prefix]\n",
      " |  number       map number (integer)\n",
      " |  title        the map title\n",
      " |  image        URL of the image map for the pathway\n",
      " |  link         URL of information about the pathway\n",
      " |  entries      Dictionary of entries in the pathway, keyed by node ID\n",
      " |  reactions    Set of reactions in the pathway\n",
      " |  \n",
      " |  The name attribute has a restricted format, so we make it a property and\n",
      " |  enforce the formatting.\n",
      " |  \n",
      " |  The Pathway object is the only allowed route for adding/removing\n",
      " |  Entry, Reaction, or Relation elements.\n",
      " |  \n",
      " |  Entries are held in a dictionary and keyed by the node ID for the\n",
      " |  pathway graph - this allows for ready access via the Reaction/Relation\n",
      " |  etc. elements.  Entries must be added before reference by any other\n",
      " |  element.\n",
      " |  \n",
      " |  Reactions are held in a dictionary, keyed by node ID for the path.\n",
      " |  The elements referred to in the reaction must be added before the\n",
      " |  reaction itself.\n",
      " |  \n",
      " |  Methods defined here:\n",
      " |  \n",
      " |  __init__(self)\n",
      " |  \n",
      " |  __str__(self)\n",
      " |      Returns a readable summary description string.\n",
      " |  \n",
      " |  add_entry(self, entry)\n",
      " |      Add an Entry element to the pathway.\n",
      " |  \n",
      " |  add_reaction(self, reaction)\n",
      " |      Add a Reaction element to the pathway.\n",
      " |  \n",
      " |  add_relation(self, relation)\n",
      " |      Add a Relation element to the pathway.\n",
      " |  \n",
      " |  get_KGML(self)\n",
      " |      Return the pathway as a string in prettified KGML format.\n",
      " |  \n",
      " |  remove_entry(self, entry)\n",
      " |      Remove an Entry element from the pathway.\n",
      " |  \n",
      " |  remove_reaction(self, reaction)\n",
      " |      Remove a Reaction element from the pathway.\n",
      " |  \n",
      " |  remove_relation(self, relation)\n",
      " |      Remove a Relation element from the pathway.\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Data descriptors defined here:\n",
      " |  \n",
      " |  __dict__\n",
      " |      dictionary for instance variables (if defined)\n",
      " |  \n",
      " |  __weakref__\n",
      " |      list of weak references to the object (if defined)\n",
      " |  \n",
      " |  bounds\n",
      " |      Coordinate bounds for all Graphics elements in the Pathway.\n",
      " |      \n",
      " |      Returns the [(xmin, ymin), (xmax, ymax)] coordinates for all\n",
      " |      Graphics elements in the Pathway\n",
      " |  \n",
      " |  compounds\n",
      " |      Get a list of entries of type compound.\n",
      " |  \n",
      " |  element\n",
      " |      Return the Pathway as a valid KGML element.\n",
      " |  \n",
      " |  genes\n",
      " |      Get a list of entries of type gene.\n",
      " |  \n",
      " |  maps\n",
      " |      Get a list of entries of type map.\n",
      " |  \n",
      " |  name\n",
      " |      The KEGGID for the pathway map.\n",
      " |  \n",
      " |  number\n",
      " |      The KEGG map number.\n",
      " |  \n",
      " |  orthologs\n",
      " |      Get a list of entries of type ortholog.\n",
      " |  \n",
      " |  reaction_entries\n",
      " |      Get a list of entries corresponding to each reaction\n",
      " |      in the pathway.\n",
      " |  \n",
      " |  reactions\n",
      " |      Get a list of reactions in the pathway.\n",
      " |  \n",
      " |  relations\n",
      " |      Get a list of relations in the pathway.\n",
      "\n"
     ]
    }
   ],
   "source": [
    "help(pathway)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "     hash()                help()                repr()                str()\n",
       "     .add_component()      .add_graphics()       .alt                  .bounds\n",
       "     .components           .element              .graphics             .id\n",
       "     .image                .is_reactant          .link                 .name\n",
       "     .reaction             .remove_component()   .remove_graphics()    .type"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "see(pathway.compounds[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "     hash()      help()      repr()      str()       .bgcolor    .bounds\n",
       "     .centre     .coords     .element    .fgcolor    .height     .name\n",
       "     .type       .width      .x          .y"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "see(pathway.compounds[0].graphics[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "671.0"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pathway.compounds[0].graphics[0].y"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    ""
   ]
  }
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