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Add notebook - converting biopax to bel
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References #13
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@cthoyt
cthoyt committed Mar 15, 2018
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271 changes: 271 additions & 0 deletions Converting BioPAX to BEL.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Converting BioPAX to BEL\n",
"\n",
"**Author:** [Charles Tapley Hoyt](https://github.com/cthoyt/)\n",
"\n",
"**Estimated Run Time:** 5 seconds\n",
"\n",
"This notebook shows how a [WikiPathways](https://www.wikipathways.org) entry, distributed as [BioPAX](http://www.biopax.org/), can be loaded into PyBEL using [INDRA](http://indra.readthedocs.io/en/latest/)."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Imports"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import sys\n",
"import os\n",
"import time\n",
"from urllib.request import urlretrieve\n",
"\n",
"import indra.util.get_version\n",
"import pybel\n",
"import pybel_tools\n",
"from pybel_tools.visualization import to_jupyter"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Environment"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"3.6.3 (default, Oct 9 2017, 09:47:56) \n",
"[GCC 4.2.1 Compatible Apple LLVM 9.0.0 (clang-900.0.37)]\n"
]
}
],
"source": [
"print(sys.version)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Thu Mar 15 15:02:01 2018\n"
]
}
],
"source": [
"print(time.asctime())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Dependencies"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'0.11.2-dev'"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pybel.utils.get_version()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'0.5.2-dev'"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pybel_tools.utils.get_version()"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"\"1.5.0-b'dcf2f45592f9c96b58622f42ba58ca342157488d'\""
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"indra.util.get_version.get_version()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Data\n",
"\n",
"The [apoptosis pathway](https://www.wikipathways.org/index.php/Pathway:WP254) is downloaded from WikiPathways to the current user's downloads folder."
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"apoptosis_url = 'https://www.wikipathways.org//wpi/wpi.php?action=downloadFile&type=owl&pwTitle=Pathway:WP254&oldid=95107'"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"apoptosis_path = os.path.join(os.path.expanduser('~'), 'Downloads', 'WP254_95107.owl')"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"if not os.path.exists(apoptosis_path):\n",
" urlretrieve(apoptosis_url, apoptosis_path)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Conversion\n",
"\n",
"A file path is given to [`from_biopax`](http://pybel.readthedocs.io/en/latest/io.html#pybel.io.indra.from_biopax)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"ERROR: [2018-03-15 15:02:04] indra/biopax - Could not open data file /Users/cthoyt/Downloads/WP254_95107.owl\n"
]
},
{
"ename": "JavaException",
"evalue": "JVM exception occurred: Label neither found, nor generated: controller PE",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mJavaException\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-10-36cbc7b280c9>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_cell_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'time'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m''\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'\\ngraph = pybel.from_biopax(apoptosis_path)'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m/usr/local/lib/python3.6/site-packages/IPython/core/interactiveshell.py\u001b[0m in \u001b[0;36mrun_cell_magic\u001b[0;34m(self, magic_name, line, cell)\u001b[0m\n\u001b[1;32m 2115\u001b[0m \u001b[0mmagic_arg_s\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvar_expand\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mline\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstack_depth\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2116\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuiltin_trap\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2117\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmagic_arg_s\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2118\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2119\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m<decorator-gen-60>\u001b[0m in \u001b[0;36mtime\u001b[0;34m(self, line, cell, local_ns)\u001b[0m\n",
"\u001b[0;32m/usr/local/lib/python3.6/site-packages/IPython/core/magic.py\u001b[0m in \u001b[0;36m<lambda>\u001b[0;34m(f, *a, **k)\u001b[0m\n\u001b[1;32m 186\u001b[0m \u001b[0;31m# but it's overkill for just that one bit of state.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 187\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mmagic_deco\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 188\u001b[0;31m \u001b[0mcall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 189\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 190\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/usr/local/lib/python3.6/site-packages/IPython/core/magics/execution.py\u001b[0m in \u001b[0;36mtime\u001b[0;34m(self, line, cell, local_ns)\u001b[0m\n\u001b[1;32m 1191\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1192\u001b[0m \u001b[0mst\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mclock2\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1193\u001b[0;31m \u001b[0mexec\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcode\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mglob\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlocal_ns\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1194\u001b[0m \u001b[0mend\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mclock2\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1195\u001b[0m \u001b[0mout\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m<timed exec>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32m/Users/cthoyt/dev/pybel/src/pybel/io/indra.py\u001b[0m in \u001b[0;36mfrom_biopax\u001b[0;34m(path, name, version, description)\u001b[0m\n\u001b[1;32m 115\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mindra\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msources\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbiopax\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbiopax_api\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mprocess_owl\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 116\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 117\u001b[0;31m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprocess_owl\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 118\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 119\u001b[0m return from_indra_statements(\n",
"\u001b[0;32m/Users/cthoyt/dev/indra/indra/sources/biopax/biopax_api.py\u001b[0m in \u001b[0;36mprocess_owl\u001b[0;34m(owl_filename)\u001b[0m\n\u001b[1;32m 158\u001b[0m \"\"\"\n\u001b[1;32m 159\u001b[0m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpcc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mowl_to_model\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mowl_filename\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 160\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mprocess_model\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodel\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 161\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 162\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/cthoyt/dev/indra/indra/sources/biopax/biopax_api.py\u001b[0m in \u001b[0;36mprocess_model\u001b[0;34m(model)\u001b[0m\n\u001b[1;32m 175\u001b[0m \"\"\"\n\u001b[1;32m 176\u001b[0m \u001b[0mbp\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mBiopaxProcessor\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodel\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 177\u001b[0;31m \u001b[0mbp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_modifications\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 178\u001b[0m \u001b[0mbp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_regulate_activities\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 179\u001b[0m \u001b[0mbp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_regulate_amounts\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/cthoyt/dev/indra/indra/sources/biopax/processor.py\u001b[0m in \u001b[0;36mget_modifications\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 107\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mmodtype\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'modification'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 108\u001b[0m \u001b[0;32mcontinue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 109\u001b[0;31m \u001b[0mstmts\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_get_generic_modification\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodclass\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 110\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstatements\u001b[0m \u001b[0;34m+=\u001b[0m \u001b[0mstmts\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 111\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/cthoyt/dev/indra/indra/sources/biopax/processor.py\u001b[0m in \u001b[0;36m_get_generic_modification\u001b[0;34m(self, mod_class)\u001b[0m\n\u001b[1;32m 635\u001b[0m \u001b[0mmod_filter\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmod_type\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m5\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 636\u001b[0m \u001b[0;31m# Start with a generic modification pattern\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 637\u001b[0;31m \u001b[0mp\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mBiopaxProcessor\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_construct_modification_pattern\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 638\u001b[0m p.add(mcc(mod_gain_const, mod_filter),\n\u001b[1;32m 639\u001b[0m \"input simple PE\", \"output simple PE\")\n",
"\u001b[0;32m/Users/cthoyt/dev/indra/indra/sources/biopax/processor.py\u001b[0m in \u001b[0;36m_construct_modification_pattern\u001b[0;34m()\u001b[0m\n\u001b[1;32m 773\u001b[0m 'controller PE')\n\u001b[1;32m 774\u001b[0m \u001b[0;31m# Getting the control itself\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 775\u001b[0;31m \u001b[0mp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0madd\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcb\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpeToControl\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"controller PE\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"Control\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 776\u001b[0m \u001b[0;31m# Link the control to the conversion that it controls\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 777\u001b[0m \u001b[0mp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0madd\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcb\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcontrolToConv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"Control\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"Conversion\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32mjnius/jnius_export_class.pxi\u001b[0m in \u001b[0;36mjnius.JavaMultipleMethod.__call__\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32mjnius/jnius_export_class.pxi\u001b[0m in \u001b[0;36mjnius.JavaMethod.__call__\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32mjnius/jnius_export_class.pxi\u001b[0m in \u001b[0;36mjnius.JavaMethod.call_method\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32mjnius/jnius_utils.pxi\u001b[0m in \u001b[0;36mjnius.check_exception\u001b[0;34m()\u001b[0m\n",
"\u001b[0;31mJavaException\u001b[0m: JVM exception occurred: Label neither found, nor generated: controller PE"
]
}
],
"source": [
"%%time\n",
"\n",
"graph = pybel.from_biopax(apoptosis_path)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"to_jupyter(graph)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.3"
}
},
"nbformat": 4,
"nbformat_minor": 1
}

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