example.ipynb

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   "execution_count": 5,
   "id": "2c0d6b40-fdb4-4239-b68c-06d2b2a75370",
   "metadata": {},
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    {
     "data": {
      "text/plain": [
       "<module 'encode_api.encode' from '/n/data1/hms/dbmi/park/sandra/ctDNA_loci/fragment_git/encode_api/encode.py'>"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from encode_api import encode\n",
    "import importlib\n",
    "\n",
    "\n",
    "import encode_api.encode\n",
    "importlib.reload(encode_api.encode)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "47a84925-9c80-440a-8be2-6570109a652a",
   "metadata": {},
   "source": [
    "### ENCODE api supported feature sets :\n",
    "```\n",
    "histone_marks = [\"H3K4me3\", \"H3K4me2\", \"H3K4me1\", \"H3K27ac\", \"H3K9ac\", \"H3K36me3\",\n",
    "                 \"H3K27me3\", \"H3K9me3\"]\n",
    "TF_marks = ['CTCF', 'POLR2A']\n",
    "DNase = ['DNase']\n",
    "gene = ['transcription']\n",
    "\n",
    "```\n",
    "### To use this API, just enter the features starting from the 4th argument of ```encode.FeatureConfig```. Feature names should be exact same name as the feature in the list above "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "062b152f-87a0-4958-ba79-1021a8670a97",
   "metadata": {},
   "source": [
    "#### if you know exact tissue ontology available in ENCODE (2nd arg should be True; if you pass 3rd arg as False it will search for tissue samples):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "c8fafb33-6f09-4055-a7fe-c1e9e5def172",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://www.encodeproject.org/search/?type=Experiment&status=released&assay_title=Histone+ChIP-seq&biosample_ontology.classification=tissue&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&replicates.library.biosample.perturbed=false&biosample_ontology.term_name=prostate+gland&award.project=ENCODE&target.label=H3K4me3&frame=embedded&format=json\n"
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
       "      <th>term_name</th>\n",
       "      <th>cell_slims</th>\n",
       "      <th>developmental_slims</th>\n",
       "      <th>summary</th>\n",
       "      <th>dataset</th>\n",
       "      <th>assay</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>prostate gland</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm, mesoderm]</td>\n",
       "      <td>male adult (37 years)</td>\n",
       "      <td>/experiments/ENCSR153NDQ/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>prostate gland</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm, mesoderm]</td>\n",
       "      <td>male adult (54 years)</td>\n",
       "      <td>/experiments/ENCSR748RBT/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        organ_slims           system_slims       term_name cell_slims  \\\n",
       "0  [prostate gland]  [reproductive system]  prostate gland         []   \n",
       "1  [prostate gland]  [reproductive system]  prostate gland         []   \n",
       "\n",
       "    developmental_slims                summary                    dataset  \\\n",
       "0  [endoderm, mesoderm]  male adult (37 years)  /experiments/ENCSR153NDQ/   \n",
       "1  [endoderm, mesoderm]  male adult (54 years)  /experiments/ENCSR748RBT/   \n",
       "\n",
       "              assay  \n",
       "0  Histone ChIP-seq  \n",
       "1  Histone ChIP-seq  "
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      "\n",
      "Enter the indices of rows to use :  0 1\n"
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       "      <th>dataset</th>\n",
       "      <th>project</th>\n",
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       "      <th>output_type</th>\n",
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       "      <th>cloud_metadata</th>\n",
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       "  <tbody>\n",
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       "      <th>0</th>\n",
       "      <td>/files/ENCFF834IDA/</td>\n",
       "      <td>/experiments/ENCSR153NDQ/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>signal p-value</td>\n",
       "      <td>H3K4me3</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm, mesoderm]</td>\n",
       "      <td>male adult (37 years)</td>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>prostate gland</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/09...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>/files/ENCFF937OWO/</td>\n",
       "      <td>/experiments/ENCSR153NDQ/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>signal p-value</td>\n",
       "      <td>H3K4me3</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm, mesoderm]</td>\n",
       "      <td>male adult (37 years)</td>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>prostate gland</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/09...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>/files/ENCFF143VBO/</td>\n",
       "      <td>/experiments/ENCSR153NDQ/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[2]</td>\n",
       "      <td>signal p-value</td>\n",
       "      <td>H3K4me3</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm, mesoderm]</td>\n",
       "      <td>male adult (37 years)</td>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>prostate gland</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/09...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>/files/ENCFF514DXI/</td>\n",
       "      <td>/experiments/ENCSR748RBT/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[2]</td>\n",
       "      <td>signal p-value</td>\n",
       "      <td>H3K4me3</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm, mesoderm]</td>\n",
       "      <td>male adult (54 years)</td>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>prostate gland</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/09...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>/files/ENCFF300OWT/</td>\n",
       "      <td>/experiments/ENCSR748RBT/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>signal p-value</td>\n",
       "      <td>H3K4me3</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm, mesoderm]</td>\n",
       "      <td>male adult (54 years)</td>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>prostate gland</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/09...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>/files/ENCFF194LKT/</td>\n",
       "      <td>/experiments/ENCSR748RBT/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>signal p-value</td>\n",
       "      <td>H3K4me3</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm, mesoderm]</td>\n",
       "      <td>male adult (54 years)</td>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>prostate gland</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/09...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                  file                    dataset  project  \\\n",
       "0  /files/ENCFF834IDA/  /experiments/ENCSR153NDQ/  ENCODE4   \n",
       "1  /files/ENCFF937OWO/  /experiments/ENCSR153NDQ/  ENCODE4   \n",
       "2  /files/ENCFF143VBO/  /experiments/ENCSR153NDQ/  ENCODE4   \n",
       "3  /files/ENCFF514DXI/  /experiments/ENCSR748RBT/  ENCODE4   \n",
       "4  /files/ENCFF300OWT/  /experiments/ENCSR748RBT/  ENCODE4   \n",
       "5  /files/ENCFF194LKT/  /experiments/ENCSR748RBT/  ENCODE4   \n",
       "\n",
       "  biological_replicates     output_type   target cell_slims  \\\n",
       "0                   [1]  signal p-value  H3K4me3         []   \n",
       "1                [1, 2]  signal p-value  H3K4me3         []   \n",
       "2                   [2]  signal p-value  H3K4me3         []   \n",
       "3                   [2]  signal p-value  H3K4me3         []   \n",
       "4                [1, 2]  signal p-value  H3K4me3         []   \n",
       "5                   [1]  signal p-value  H3K4me3         []   \n",
       "\n",
       "    developmental_slims                summary       organ_slims  \\\n",
       "0  [endoderm, mesoderm]  male adult (37 years)  [prostate gland]   \n",
       "1  [endoderm, mesoderm]  male adult (37 years)  [prostate gland]   \n",
       "2  [endoderm, mesoderm]  male adult (37 years)  [prostate gland]   \n",
       "3  [endoderm, mesoderm]  male adult (54 years)  [prostate gland]   \n",
       "4  [endoderm, mesoderm]  male adult (54 years)  [prostate gland]   \n",
       "5  [endoderm, mesoderm]  male adult (54 years)  [prostate gland]   \n",
       "\n",
       "            system_slims       term_name  \\\n",
       "0  [reproductive system]  prostate gland   \n",
       "1  [reproductive system]  prostate gland   \n",
       "2  [reproductive system]  prostate gland   \n",
       "3  [reproductive system]  prostate gland   \n",
       "4  [reproductive system]  prostate gland   \n",
       "5  [reproductive system]  prostate gland   \n",
       "\n",
       "                                      cloud_metadata  \n",
       "0  https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "1  https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "2  https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "3  https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "4  https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "5  https://encode-public.s3.amazonaws.com/2020/09...  "
      ]
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      "\n",
      "Enter the indices of rows to use :  1 4\n"
     ]
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://www.encodeproject.org/search/?type=Experiment&status=released&assay_title=DNase-seq&biosample_ontology.classification=tissue&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&replicates.library.biosample.perturbed=false&biosample_ontology.term_name=prostate+gland&award.project=ENCODE&frame=embedded&format=json\n"
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       "      <th></th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
       "      <th>term_name</th>\n",
       "      <th>cell_slims</th>\n",
       "      <th>developmental_slims</th>\n",
       "      <th>summary</th>\n",
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       "      <th>assay</th>\n",
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       "  <tbody>\n",
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       "      <th>0</th>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>prostate gland</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm, mesoderm]</td>\n",
       "      <td>male adult (37 years)</td>\n",
       "      <td>/experiments/ENCSR564FZH/</td>\n",
       "      <td>DNase-seq</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "        organ_slims           system_slims       term_name cell_slims  \\\n",
       "0  [prostate gland]  [reproductive system]  prostate gland         []   \n",
       "\n",
       "    developmental_slims                summary                    dataset  \\\n",
       "0  [endoderm, mesoderm]  male adult (37 years)  /experiments/ENCSR564FZH/   \n",
       "\n",
       "       assay  \n",
       "0  DNase-seq  "
      ]
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       "      <th>file</th>\n",
       "      <th>dataset</th>\n",
       "      <th>project</th>\n",
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       "      <th>output_type</th>\n",
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       "      <th>developmental_slims</th>\n",
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       "      <th>cloud_metadata</th>\n",
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       "      <th>0</th>\n",
       "      <td>/files/ENCFF865IXT/</td>\n",
       "      <td>/experiments/ENCSR564FZH/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm, mesoderm]</td>\n",
       "      <td>male adult (37 years)</td>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>prostate gland</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/10...</td>\n",
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      ],
      "text/plain": [
       "                  file                    dataset  project  \\\n",
       "0  /files/ENCFF865IXT/  /experiments/ENCSR564FZH/  ENCODE4   \n",
       "\n",
       "  biological_replicates                   output_type cell_slims  \\\n",
       "0                   [1]  read-depth normalized signal         []   \n",
       "\n",
       "    developmental_slims                summary       organ_slims  \\\n",
       "0  [endoderm, mesoderm]  male adult (37 years)  [prostate gland]   \n",
       "\n",
       "            system_slims       term_name  \\\n",
       "0  [reproductive system]  prostate gland   \n",
       "\n",
       "                                      cloud_metadata  \n",
       "0  https://encode-public.s3.amazonaws.com/2020/10...  "
      ]
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      "\n",
      "Enter the indices of rows to use :  0\n"
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     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://www.encodeproject.org/search/?type=Experiment&status=released&assay_title=TF+ChIP-seq&biosample_ontology.classification=tissue&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&replicates.library.biosample.perturbed=false&biosample_ontology.term_name=prostate+gland&award.project=ENCODE&target.label=POLR2A&frame=embedded&format=json\n"
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
       "      <th>term_name</th>\n",
       "      <th>cell_slims</th>\n",
       "      <th>developmental_slims</th>\n",
       "      <th>summary</th>\n",
       "      <th>dataset</th>\n",
       "      <th>assay</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>prostate gland</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm, mesoderm]</td>\n",
       "      <td>male adult (54 years)</td>\n",
       "      <td>/experiments/ENCSR122LGV/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
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       "        organ_slims           system_slims       term_name cell_slims  \\\n",
       "0  [prostate gland]  [reproductive system]  prostate gland         []   \n",
       "1  [prostate gland]  [reproductive system]  prostate gland         []   \n",
       "\n",
       "    developmental_slims                summary                    dataset  \\\n",
       "0  [endoderm, mesoderm]  male adult (54 years)  /experiments/ENCSR122LGV/   \n",
       "1  [endoderm, mesoderm]  male adult (37 years)  /experiments/ENCSR911JAX/   \n",
       "\n",
       "         assay  \n",
       "0  TF ChIP-seq  \n",
       "1  TF ChIP-seq  "
      ]
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       "                  file                    dataset  project  \\\n",
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       "\n",
       "  biological_replicates     output_type  target cell_slims  \\\n",
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       "\n",
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       "0  [endoderm, mesoderm]  male adult (54 years)  [prostate gland]   \n",
       "1  [endoderm, mesoderm]  male adult (37 years)  [prostate gland]   \n",
       "\n",
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       "\n",
       "                                      cloud_metadata  \n",
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     "text": [
      "https://www.encodeproject.org/search/?type=Experiment&status=released&assay_title=TF+ChIP-seq&biosample_ontology.classification=tissue&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&replicates.library.biosample.perturbed=false&biosample_ontology.term_name=prostate+gland&award.project=ENCODE&target.label=CTCF&frame=embedded&format=json\n"
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       "        organ_slims           system_slims       term_name cell_slims  \\\n",
       "0  [prostate gland]  [reproductive system]  prostate gland         []   \n",
       "1  [prostate gland]  [reproductive system]  prostate gland         []   \n",
       "2  [prostate gland]  [reproductive system]  prostate gland         []   \n",
       "3  [prostate gland]  [reproductive system]  prostate gland         []   \n",
       "\n",
       "    developmental_slims                summary                    dataset  \\\n",
       "0  [endoderm, mesoderm]  male adult (37 years)  /experiments/ENCSR946MNG/   \n",
       "1  [endoderm, mesoderm]  male adult (54 years)  /experiments/ENCSR230ORT/   \n",
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       "3  [mesoderm, endoderm]  male adult (54 years)  /experiments/ENCSR829HTO/   \n",
       "\n",
       "         assay  \n",
       "0  TF ChIP-seq  \n",
       "1  TF ChIP-seq  \n",
       "2  TF ChIP-seq  \n",
       "3  TF ChIP-seq  "
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       "    <tr>\n",
       "      <th>6</th>\n",
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      ],
      "text/plain": [
       "                  file                    dataset  project  \\\n",
       "0  /files/ENCFF900BDC/  /experiments/ENCSR230ORT/  ENCODE4   \n",
       "1  /files/ENCFF563NCU/  /experiments/ENCSR230ORT/  ENCODE4   \n",
       "2  /files/ENCFF412WWE/  /experiments/ENCSR230ORT/  ENCODE4   \n",
       "3  /files/ENCFF400NQB/  /experiments/ENCSR230ORT/  ENCODE4   \n",
       "4  /files/ENCFF351NKT/  /experiments/ENCSR720USO/  ENCODE4   \n",
       "5  /files/ENCFF771ZYH/  /experiments/ENCSR829HTO/  ENCODE4   \n",
       "6  /files/ENCFF703KDQ/  /experiments/ENCSR946MNG/  ENCODE4   \n",
       "\n",
       "  biological_replicates                         output_type target cell_slims  \\\n",
       "0                   [2]               IDR thresholded peaks   CTCF         []   \n",
       "1                   [1]               IDR thresholded peaks   CTCF         []   \n",
       "2                [1, 2]  conservative IDR thresholded peaks   CTCF         []   \n",
       "3                [1, 2]               IDR thresholded peaks   CTCF         []   \n",
       "4                   [1]               IDR thresholded peaks   CTCF         []   \n",
       "5                   [1]               IDR thresholded peaks   CTCF         []   \n",
       "6                   [1]               IDR thresholded peaks   CTCF         []   \n",
       "\n",
       "    developmental_slims                summary       organ_slims  \\\n",
       "0  [endoderm, mesoderm]  male adult (54 years)  [prostate gland]   \n",
       "1  [endoderm, mesoderm]  male adult (54 years)  [prostate gland]   \n",
       "2  [endoderm, mesoderm]  male adult (54 years)  [prostate gland]   \n",
       "3  [endoderm, mesoderm]  male adult (54 years)  [prostate gland]   \n",
       "4  [mesoderm, endoderm]  male adult (37 years)  [prostate gland]   \n",
       "5  [mesoderm, endoderm]  male adult (54 years)  [prostate gland]   \n",
       "6  [endoderm, mesoderm]  male adult (37 years)  [prostate gland]   \n",
       "\n",
       "            system_slims       term_name  \\\n",
       "0  [reproductive system]  prostate gland   \n",
       "1  [reproductive system]  prostate gland   \n",
       "2  [reproductive system]  prostate gland   \n",
       "3  [reproductive system]  prostate gland   \n",
       "4  [reproductive system]  prostate gland   \n",
       "5  [reproductive system]  prostate gland   \n",
       "6  [reproductive system]  prostate gland   \n",
       "\n",
       "                                      cloud_metadata  \n",
       "0  https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "1  https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "2  https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "3  https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "4  https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "5  https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "6  https://encode-public.s3.amazonaws.com/2020/09...  "
      ]
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      "\n",
      "Enter the indices of rows to use :  3 4 5 6\n"
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     "text": [
      "https://www.encodeproject.org/search/?type=Experiment&status=released&assay_title=total+RNA-seq&assay_title=polyA+plus+RNA-seq&biosample_ontology.classification=tissue&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&replicates.library.biosample.perturbed=false&biosample_ontology.term_name=prostate+gland&award.project=ENCODE&frame=embedded&format=json\n"
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       "      <td>total RNA-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>prostate gland</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm, mesoderm]</td>\n",
       "      <td>male adult (37 years)</td>\n",
       "      <td>/experiments/ENCSR495HDM/</td>\n",
       "      <td>total RNA-seq</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        organ_slims           system_slims       term_name cell_slims  \\\n",
       "0  [prostate gland]  [reproductive system]  prostate gland         []   \n",
       "1  [prostate gland]  [reproductive system]  prostate gland         []   \n",
       "\n",
       "    developmental_slims                summary                    dataset  \\\n",
       "0  [endoderm, mesoderm]  male adult (54 years)  /experiments/ENCSR701TST/   \n",
       "1  [endoderm, mesoderm]  male adult (37 years)  /experiments/ENCSR495HDM/   \n",
       "\n",
       "           assay  \n",
       "0  total RNA-seq  \n",
       "1  total RNA-seq  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "\n",
      "Enter the indices of rows to use :  0 1\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>file</th>\n",
       "      <th>dataset</th>\n",
       "      <th>project</th>\n",
       "      <th>biological_replicates</th>\n",
       "      <th>output_type</th>\n",
       "      <th>cell_slims</th>\n",
       "      <th>developmental_slims</th>\n",
       "      <th>summary</th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
       "      <th>term_name</th>\n",
       "      <th>cloud_metadata</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>/files/ENCFF042VIA/</td>\n",
       "      <td>/experiments/ENCSR495HDM/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>gene quantifications</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm, mesoderm]</td>\n",
       "      <td>male adult (37 years)</td>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>prostate gland</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>/files/ENCFF485OGN/</td>\n",
       "      <td>/experiments/ENCSR701TST/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>gene quantifications</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm, mesoderm]</td>\n",
       "      <td>male adult (54 years)</td>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>prostate gland</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                  file                    dataset  project  \\\n",
       "0  /files/ENCFF042VIA/  /experiments/ENCSR495HDM/  ENCODE4   \n",
       "1  /files/ENCFF485OGN/  /experiments/ENCSR701TST/  ENCODE4   \n",
       "\n",
       "  biological_replicates           output_type cell_slims  \\\n",
       "0                   [1]  gene quantifications         []   \n",
       "1                   [1]  gene quantifications         []   \n",
       "\n",
       "    developmental_slims                summary       organ_slims  \\\n",
       "0  [endoderm, mesoderm]  male adult (37 years)  [prostate gland]   \n",
       "1  [endoderm, mesoderm]  male adult (54 years)  [prostate gland]   \n",
       "\n",
       "            system_slims       term_name  \\\n",
       "0  [reproductive system]  prostate gland   \n",
       "1  [reproductive system]  prostate gland   \n",
       "\n",
       "                                      cloud_metadata  \n",
       "0  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "1  https://encode-public.s3.amazonaws.com/2020/07...  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "\n",
      "Enter the indices of rows to use :  0 1\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "defaultdict(list,\n",
       "            {'H3K4me3': ['https://encode-public.s3.amazonaws.com/2020/09/24/4d3da9ba-7b18-4b70-80d1-5e1cf1e40464/ENCFF937OWO.bigWig',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/09/22/a57dc2a8-bf4e-4d5f-93a0-f436c1b7923d/ENCFF300OWT.bigWig'],\n",
       "             'DNase': ['https://encode-public.s3.amazonaws.com/2020/10/06/f3b2ddef-3ab9-4fb6-84e8-f56db7878453/ENCFF865IXT.bigWig'],\n",
       "             'POLR2A': ['https://encode-public.s3.amazonaws.com/2020/12/30/2fcfc23c-ad67-4757-8a23-b34e77618f56/ENCFF152LGU.bigWig',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/12/01/98b1b0eb-369a-4439-be30-58cd276c5d96/ENCFF100FTA.bigWig'],\n",
       "             'CTCF': ['https://encode-public.s3.amazonaws.com/2020/09/24/1e953256-aa80-4397-803f-a298c2bfc390/ENCFF400NQB.bed.gz',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/09/01/81710556-6615-4cc2-b3ef-cd40df5f9421/ENCFF351NKT.bed.gz',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/09/01/392b4a9e-c4fe-4c36-abde-c7f20d21f14d/ENCFF771ZYH.bed.gz',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/09/24/e56c35ea-7d69-42fb-9903-860a434a4b72/ENCFF703KDQ.bed.gz'],\n",
       "             'transcription': ['https://encode-public.s3.amazonaws.com/2020/07/14/3f67db5f-ff26-4ce7-993b-893b64b9af80/ENCFF042VIA.tsv',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/07/14/d95a027d-ca9b-4f55-b66a-e6a54f92335e/ENCFF485OGN.tsv']})"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "c = encode.FeatureConfig('prostate gland',  True, False, \"H3K4me3\", \"DNase\", \"POLR2A\", \"CTCF\", \"transcription\")\n",
    "results = c.parse_url(rfa='ENCODE4') # you can change it to ENCODE3, to restrict files processed from one of ENCODE3 or ENCODE4\n",
    "results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "c0d7d3a1-70cf-4980-9837-0a2c45fc3625",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "defaultdict(list,\n",
       "            {'H3K4me3': ['https://encode-public.s3.amazonaws.com/2020/09/24/4d3da9ba-7b18-4b70-80d1-5e1cf1e40464/ENCFF937OWO.bigWig',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/09/22/a57dc2a8-bf4e-4d5f-93a0-f436c1b7923d/ENCFF300OWT.bigWig'],\n",
       "             'DNase': ['https://encode-public.s3.amazonaws.com/2020/10/06/f3b2ddef-3ab9-4fb6-84e8-f56db7878453/ENCFF865IXT.bigWig'],\n",
       "             'POLR2A': ['https://encode-public.s3.amazonaws.com/2020/12/30/2fcfc23c-ad67-4757-8a23-b34e77618f56/ENCFF152LGU.bigWig',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/12/01/98b1b0eb-369a-4439-be30-58cd276c5d96/ENCFF100FTA.bigWig'],\n",
       "             'CTCF': ['https://encode-public.s3.amazonaws.com/2020/09/24/1e953256-aa80-4397-803f-a298c2bfc390/ENCFF400NQB.bed.gz',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/09/01/81710556-6615-4cc2-b3ef-cd40df5f9421/ENCFF351NKT.bed.gz',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/09/01/392b4a9e-c4fe-4c36-abde-c7f20d21f14d/ENCFF771ZYH.bed.gz',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/09/24/e56c35ea-7d69-42fb-9903-860a434a4b72/ENCFF703KDQ.bed.gz'],\n",
       "             'transcription': ['https://encode-public.s3.amazonaws.com/2020/07/14/3f67db5f-ff26-4ce7-993b-893b64b9af80/ENCFF042VIA.tsv',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/07/14/d95a027d-ca9b-4f55-b66a-e6a54f92335e/ENCFF485OGN.tsv']})"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "results"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3da00da0-247f-4a8d-bfa9-cec2148ad391",
   "metadata": {},
   "source": [
    "#### try to find cell line sample if tissue sample is not available for the features"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 109,
   "id": "02c63267-d236-40ac-9ebc-893bcd6094e8",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://www.encodeproject.org/search/?type=Experiment&status=released&assay_title=total+RNA-seq&assay_title=polyA+plus+RNA-seq&biosample_ontology.classification=cell+line&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&replicates.library.biosample.perturbed=false&searchTerm=prostate&award.project=ENCODE&frame=embedded&format=json\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
       "      <th>term_name</th>\n",
       "      <th>cell_slims</th>\n",
       "      <th>developmental_slims</th>\n",
       "      <th>summary</th>\n",
       "      <th>dataset</th>\n",
       "      <th>assay</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>PC-3</td>\n",
       "      <td>[cancer cell]</td>\n",
       "      <td>[mesoderm, endoderm]</td>\n",
       "      <td></td>\n",
       "      <td>/experiments/ENCSR648KDM/</td>\n",
       "      <td>total RNA-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>PC-3</td>\n",
       "      <td>[cancer cell]</td>\n",
       "      <td>[mesoderm, endoderm]</td>\n",
       "      <td></td>\n",
       "      <td>/experiments/ENCSR420NLC/</td>\n",
       "      <td>total RNA-seq</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        organ_slims           system_slims term_name     cell_slims  \\\n",
       "0  [prostate gland]  [reproductive system]      PC-3  [cancer cell]   \n",
       "1  [prostate gland]  [reproductive system]      PC-3  [cancer cell]   \n",
       "\n",
       "    developmental_slims summary                    dataset          assay  \n",
       "0  [mesoderm, endoderm]          /experiments/ENCSR648KDM/  total RNA-seq  \n",
       "1  [mesoderm, endoderm]          /experiments/ENCSR420NLC/  total RNA-seq  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "\n",
      "Enter the indices of rows to use :  0 1\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>file</th>\n",
       "      <th>dataset</th>\n",
       "      <th>project</th>\n",
       "      <th>biological_replicates</th>\n",
       "      <th>output_type</th>\n",
       "      <th>cell_slims</th>\n",
       "      <th>developmental_slims</th>\n",
       "      <th>summary</th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
       "      <th>term_name</th>\n",
       "      <th>cloud_metadata</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>/files/ENCFF882EWJ/</td>\n",
       "      <td>/experiments/ENCSR420NLC/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[2]</td>\n",
       "      <td>gene quantifications</td>\n",
       "      <td>[cancer cell]</td>\n",
       "      <td>[mesoderm, endoderm]</td>\n",
       "      <td></td>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>PC-3</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2021/06...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>/files/ENCFF970ZLV/</td>\n",
       "      <td>/experiments/ENCSR420NLC/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>gene quantifications</td>\n",
       "      <td>[cancer cell]</td>\n",
       "      <td>[mesoderm, endoderm]</td>\n",
       "      <td></td>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>PC-3</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2021/06...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>/files/ENCFF617JTM/</td>\n",
       "      <td>/experiments/ENCSR648KDM/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>gene quantifications</td>\n",
       "      <td>[cancer cell]</td>\n",
       "      <td>[mesoderm, endoderm]</td>\n",
       "      <td></td>\n",
       "      <td>[prostate gland]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>PC-3</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/10...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                  file                    dataset  project  \\\n",
       "0  /files/ENCFF882EWJ/  /experiments/ENCSR420NLC/  ENCODE4   \n",
       "1  /files/ENCFF970ZLV/  /experiments/ENCSR420NLC/  ENCODE4   \n",
       "2  /files/ENCFF617JTM/  /experiments/ENCSR648KDM/  ENCODE4   \n",
       "\n",
       "  biological_replicates           output_type     cell_slims  \\\n",
       "0                   [2]  gene quantifications  [cancer cell]   \n",
       "1                   [1]  gene quantifications  [cancer cell]   \n",
       "2                   [1]  gene quantifications  [cancer cell]   \n",
       "\n",
       "    developmental_slims summary       organ_slims           system_slims  \\\n",
       "0  [mesoderm, endoderm]          [prostate gland]  [reproductive system]   \n",
       "1  [mesoderm, endoderm]          [prostate gland]  [reproductive system]   \n",
       "2  [mesoderm, endoderm]          [prostate gland]  [reproductive system]   \n",
       "\n",
       "  term_name                                     cloud_metadata  \n",
       "0      PC-3  https://encode-public.s3.amazonaws.com/2021/06...  \n",
       "1      PC-3  https://encode-public.s3.amazonaws.com/2021/06...  \n",
       "2      PC-3  https://encode-public.s3.amazonaws.com/2020/10...  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "\n",
      "Enter the indices of rows to use :  0 1 2\n"
     ]
    }
   ],
   "source": [
    "c2 = encode.FeatureConfig('prostate',  False, True, \"transcription\", ) # change 3rd arg to True \n",
    "results2 = c2.parse_url(rfa='ENCODE4') "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 110,
   "id": "95b4f4c8-bc2a-4e63-8cf1-6a4778e92209",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "defaultdict(list,\n",
       "            {'transcription': ['https://encode-public.s3.amazonaws.com/2021/06/01/4c7dfb36-4825-4a92-808b-d963cfa388bc/ENCFF882EWJ.tsv',\n",
       "              'https://encode-public.s3.amazonaws.com/2021/06/01/639c03fd-3fc5-442d-a5d4-2badb8d1091e/ENCFF970ZLV.tsv',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/10/30/ae4ec0f6-6070-4977-93b8-befc070764b9/ENCFF617JTM.tsv']})"
      ]
     },
     "execution_count": 110,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "results2"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c60dc57c-7855-4fc7-a2ca-010328ac7968",
   "metadata": {},
   "source": [
    "#### if you are not sure about exact sample ontology available in ENCODE, change 2nd arg to False:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 114,
   "id": "8733d5e0-d3a8-41b9-bac2-b639f98ff84f",
   "metadata": {},
   "outputs": [],
   "source": [
    "c3 = encode.FeatureConfig('breast',  False, False, \"H3K4me3\", \"CTCF\", )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 115,
   "id": "c711874a-f283-4ac3-a175-4d80413cfc50",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://www.encodeproject.org/search/?type=Experiment&status=released&assay_title=Histone+ChIP-seq&biosample_ontology.classification=tissue&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&replicates.library.biosample.perturbed=false&searchTerm=breast&award.project=ENCODE&target.label=H3K4me3&frame=embedded&format=json\n"
     ]
    },
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
       "      <th>term_name</th>\n",
       "      <th>cell_slims</th>\n",
       "      <th>developmental_slims</th>\n",
       "      <th>summary</th>\n",
       "      <th>dataset</th>\n",
       "      <th>assay</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>[breast, epithelium]</td>\n",
       "      <td>[]</td>\n",
       "      <td>breast epithelium</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (53 years)</td>\n",
       "      <td>/experiments/ENCSR416AUW/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>[breast, epithelium]</td>\n",
       "      <td>[]</td>\n",
       "      <td>breast epithelium</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>male adult (37 years)</td>\n",
       "      <td>/experiments/ENCSR224STY/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>[epithelium, breast]</td>\n",
       "      <td>[]</td>\n",
       "      <td>breast epithelium</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (51 years)</td>\n",
       "      <td>/experiments/ENCSR568QQU/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "            organ_slims system_slims          term_name cell_slims  \\\n",
       "0  [breast, epithelium]           []  breast epithelium         []   \n",
       "1  [breast, epithelium]           []  breast epithelium         []   \n",
       "2  [epithelium, breast]           []  breast epithelium         []   \n",
       "\n",
       "  developmental_slims                  summary                    dataset  \\\n",
       "0                  []  female adult (53 years)  /experiments/ENCSR416AUW/   \n",
       "1                  []    male adult (37 years)  /experiments/ENCSR224STY/   \n",
       "2                  []  female adult (51 years)  /experiments/ENCSR568QQU/   \n",
       "\n",
       "              assay  \n",
       "0  Histone ChIP-seq  \n",
       "1  Histone ChIP-seq  \n",
       "2  Histone ChIP-seq  "
      ]
     },
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       "      <th>cloud_metadata</th>\n",
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       "      <th>0</th>\n",
       "      <td>/files/ENCFF449LNR/</td>\n",
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       "      <td>ENCODE4</td>\n",
       "      <td>[1, 2]</td>\n",
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       "      <td>[]</td>\n",
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       "      <td>https://encode-public.s3.amazonaws.com/2020/10...</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
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       "      <td>[]</td>\n",
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       "      <td>https://encode-public.s3.amazonaws.com/2020/10...</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
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       "      <td>ENCODE4</td>\n",
       "      <td>[2]</td>\n",
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       "      <td>H3K4me3</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (53 years)</td>\n",
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       "      <td>[]</td>\n",
       "      <td>breast epithelium</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/10...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>/files/ENCFF403VNT/</td>\n",
       "      <td>/experiments/ENCSR568QQU/</td>\n",
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       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (51 years)</td>\n",
       "      <td>[epithelium, breast]</td>\n",
       "      <td>[]</td>\n",
       "      <td>breast epithelium</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/09...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                  file                    dataset  project  \\\n",
       "0  /files/ENCFF449LNR/  /experiments/ENCSR416AUW/  ENCODE4   \n",
       "1  /files/ENCFF534QEF/  /experiments/ENCSR416AUW/  ENCODE4   \n",
       "2  /files/ENCFF200LAB/  /experiments/ENCSR416AUW/  ENCODE4   \n",
       "3  /files/ENCFF403VNT/  /experiments/ENCSR568QQU/  ENCODE4   \n",
       "\n",
       "  biological_replicates     output_type   target cell_slims  \\\n",
       "0                [1, 2]  signal p-value  H3K4me3         []   \n",
       "1                   [1]  signal p-value  H3K4me3         []   \n",
       "2                   [2]  signal p-value  H3K4me3         []   \n",
       "3                   [1]  signal p-value  H3K4me3         []   \n",
       "\n",
       "  developmental_slims                  summary           organ_slims  \\\n",
       "0                  []  female adult (53 years)  [breast, epithelium]   \n",
       "1                  []  female adult (53 years)  [breast, epithelium]   \n",
       "2                  []  female adult (53 years)  [breast, epithelium]   \n",
       "3                  []  female adult (51 years)  [epithelium, breast]   \n",
       "\n",
       "  system_slims          term_name  \\\n",
       "0           []  breast epithelium   \n",
       "1           []  breast epithelium   \n",
       "2           []  breast epithelium   \n",
       "3           []  breast epithelium   \n",
       "\n",
       "                                      cloud_metadata  \n",
       "0  https://encode-public.s3.amazonaws.com/2020/10...  \n",
       "1  https://encode-public.s3.amazonaws.com/2020/10...  \n",
       "2  https://encode-public.s3.amazonaws.com/2020/10...  \n",
       "3  https://encode-public.s3.amazonaws.com/2020/09...  "
      ]
     },
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    },
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "\n",
      "Enter the indices of rows to use :  0 2 3\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://www.encodeproject.org/search/?type=Experiment&status=released&assay_title=TF+ChIP-seq&biosample_ontology.classification=tissue&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&replicates.library.biosample.perturbed=false&searchTerm=breast&award.project=ENCODE&target.label=CTCF&frame=embedded&format=json\n"
     ]
    },
    {
     "data": {
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       "  <thead>\n",
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       "      <th></th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
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       "      <td>[breast, epithelium]</td>\n",
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       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>[epithelium, breast]</td>\n",
       "      <td>[]</td>\n",
       "      <td>breast epithelium</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (51 years)</td>\n",
       "      <td>/experiments/ENCSR661NXJ/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "            organ_slims system_slims          term_name cell_slims  \\\n",
       "0  [breast, epithelium]           []  breast epithelium         []   \n",
       "1  [breast, epithelium]           []  breast epithelium         []   \n",
       "2  [epithelium, breast]           []  breast epithelium         []   \n",
       "\n",
       "  developmental_slims                  summary                    dataset  \\\n",
       "0                  []    male adult (54 years)  /experiments/ENCSR697YIN/   \n",
       "1                  []  female adult (53 years)  /experiments/ENCSR304XUZ/   \n",
       "2                  []  female adult (51 years)  /experiments/ENCSR661NXJ/   \n",
       "\n",
       "         assay  \n",
       "0  TF ChIP-seq  \n",
       "1  TF ChIP-seq  \n",
       "2  TF ChIP-seq  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdin",
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      "\n",
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     ]
    },
    {
     "data": {
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       "      <th>0</th>\n",
       "      <td>/files/ENCFF910ACN/</td>\n",
       "      <td>/experiments/ENCSR304XUZ/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
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       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (53 years)</td>\n",
       "      <td>[breast, epithelium]</td>\n",
       "      <td>[]</td>\n",
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>/files/ENCFF530ARF/</td>\n",
       "      <td>/experiments/ENCSR661NXJ/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>IDR thresholded peaks</td>\n",
       "      <td>CTCF</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (51 years)</td>\n",
       "      <td>[epithelium, breast]</td>\n",
       "      <td>[]</td>\n",
       "      <td>breast epithelium</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/09...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                  file                    dataset  project  \\\n",
       "0  /files/ENCFF910ACN/  /experiments/ENCSR304XUZ/  ENCODE4   \n",
       "1  /files/ENCFF530ARF/  /experiments/ENCSR661NXJ/  ENCODE4   \n",
       "\n",
       "  biological_replicates            output_type target cell_slims  \\\n",
       "0                   [1]  IDR thresholded peaks   CTCF         []   \n",
       "1                   [1]  IDR thresholded peaks   CTCF         []   \n",
       "\n",
       "  developmental_slims                  summary           organ_slims  \\\n",
       "0                  []  female adult (53 years)  [breast, epithelium]   \n",
       "1                  []  female adult (51 years)  [epithelium, breast]   \n",
       "\n",
       "  system_slims          term_name  \\\n",
       "0           []  breast epithelium   \n",
       "1           []  breast epithelium   \n",
       "\n",
       "                                      cloud_metadata  \n",
       "0  https://encode-public.s3.amazonaws.com/2020/10...  \n",
       "1  https://encode-public.s3.amazonaws.com/2020/09...  "
      ]
     },
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    },
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "\n",
      "Enter the indices of rows to use :  0 1\n"
     ]
    }
   ],
   "source": [
    "results3 = c3.parse_url()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 116,
   "id": "836e5284-b77d-4f86-8d34-d5604d80f486",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "defaultdict(list,\n",
       "            {'H3K4me3': ['https://encode-public.s3.amazonaws.com/2020/10/10/a190f445-dec2-4e07-955e-da1756f10bc4/ENCFF449LNR.bigWig',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/10/10/57b16f05-6dad-42b3-be58-aeba328ca24b/ENCFF200LAB.bigWig',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/09/23/64fc5b6a-f571-46e1-863a-84a3d73ab1fb/ENCFF403VNT.bigWig'],\n",
       "             'CTCF': ['https://encode-public.s3.amazonaws.com/2020/10/10/ceaa3a29-86bb-4e42-ace8-a79bf821398f/ENCFF910ACN.bed.gz',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/09/01/29a4d2b3-6426-4c8b-9859-15df343fc1e8/ENCFF530ARF.bed.gz']})"
      ]
     },
     "execution_count": 116,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "results3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 125,
   "id": "4d46add4-6b90-4a3e-ab71-769625302b4b",
   "metadata": {},
   "outputs": [],
   "source": [
    "c4 = encode.FeatureConfig('lung',  False, False, \"H3K4me3\", \"CTCF\", )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 126,
   "id": "0436901c-0bcb-4e42-a071-d19ef59456eb",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://www.encodeproject.org/search/?type=Experiment&status=released&assay_title=Histone+ChIP-seq&biosample_ontology.classification=tissue&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&replicates.library.biosample.perturbed=false&searchTerm=lung&award.project=ENCODE&target.label=H3K4me3&frame=embedded&format=json\n"
     ]
    },
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
       "      <th>term_name</th>\n",
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       "      <th>developmental_slims</th>\n",
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       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>lower lobe of left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (60 years)</td>\n",
       "      <td>/experiments/ENCSR368BOE/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of right lung</td>\n",
       "      <td>[]</td>\n",
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       "      <td>/experiments/ENCSR385YCN/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>lower lobe of right lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (60 years)</td>\n",
       "      <td>/experiments/ENCSR788WNE/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>lower lobe of left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>female adult (59 years)</td>\n",
       "      <td>/experiments/ENCSR791BWS/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>female adult (53 years)</td>\n",
       "      <td>/experiments/ENCSR208WDY/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>female adult (51 years)</td>\n",
       "      <td>/experiments/ENCSR429VWL/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (54 years)</td>\n",
       "      <td>/experiments/ENCSR701FGA/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (37 years)</td>\n",
       "      <td>/experiments/ENCSR074WIB/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (40 years)</td>\n",
       "      <td>/experiments/ENCSR864ECD/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>female child (16 years)</td>\n",
       "      <td>/experiments/ENCSR904KDP/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>[heart]</td>\n",
       "      <td>[circulatory system]</td>\n",
       "      <td>left ventricle myocardium inferior</td>\n",
       "      <td>[]</td>\n",
       "      <td>[mesoderm]</td>\n",
       "      <td>male adult (60 years)</td>\n",
       "      <td>/experiments/ENCSR737WCC/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>[spleen, immune organ]</td>\n",
       "      <td>[digestive system, immune system]</td>\n",
       "      <td>spleen</td>\n",
       "      <td>[]</td>\n",
       "      <td>[mesoderm]</td>\n",
       "      <td>female adult (61 years)</td>\n",
       "      <td>/experiments/ENCSR981USF/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>[pancreas]</td>\n",
       "      <td>[]</td>\n",
       "      <td>pancreas</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>female adult (61 years)</td>\n",
       "      <td>/experiments/ENCSR211SBE/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "               organ_slims                       system_slims  \\\n",
       "0                   [lung]               [respiratory system]   \n",
       "1                   [lung]               [respiratory system]   \n",
       "2                   [lung]               [respiratory system]   \n",
       "3                   [lung]               [respiratory system]   \n",
       "4                   [lung]               [respiratory system]   \n",
       "5                   [lung]               [respiratory system]   \n",
       "6                   [lung]               [respiratory system]   \n",
       "7                   [lung]               [respiratory system]   \n",
       "8                   [lung]               [respiratory system]   \n",
       "9                   [lung]               [respiratory system]   \n",
       "10                 [heart]               [circulatory system]   \n",
       "11  [spleen, immune organ]  [digestive system, immune system]   \n",
       "12              [pancreas]                                 []   \n",
       "\n",
       "                             term_name cell_slims developmental_slims  \\\n",
       "0              lower lobe of left lung         []          [endoderm]   \n",
       "1             upper lobe of right lung         []          [endoderm]   \n",
       "2             lower lobe of right lung         []          [endoderm]   \n",
       "3              lower lobe of left lung         []          [endoderm]   \n",
       "4              upper lobe of left lung         []          [endoderm]   \n",
       "5              upper lobe of left lung         []          [endoderm]   \n",
       "6              upper lobe of left lung         []          [endoderm]   \n",
       "7              upper lobe of left lung         []          [endoderm]   \n",
       "8                            left lung         []          [endoderm]   \n",
       "9                            left lung         []          [endoderm]   \n",
       "10  left ventricle myocardium inferior         []          [mesoderm]   \n",
       "11                              spleen         []          [mesoderm]   \n",
       "12                            pancreas         []          [endoderm]   \n",
       "\n",
       "                    summary                    dataset             assay  \n",
       "0     male adult (60 years)  /experiments/ENCSR368BOE/  Histone ChIP-seq  \n",
       "1     male adult (60 years)  /experiments/ENCSR385YCN/  Histone ChIP-seq  \n",
       "2     male adult (60 years)  /experiments/ENCSR788WNE/  Histone ChIP-seq  \n",
       "3   female adult (59 years)  /experiments/ENCSR791BWS/  Histone ChIP-seq  \n",
       "4   female adult (53 years)  /experiments/ENCSR208WDY/  Histone ChIP-seq  \n",
       "5   female adult (51 years)  /experiments/ENCSR429VWL/  Histone ChIP-seq  \n",
       "6     male adult (54 years)  /experiments/ENCSR701FGA/  Histone ChIP-seq  \n",
       "7     male adult (37 years)  /experiments/ENCSR074WIB/  Histone ChIP-seq  \n",
       "8     male adult (40 years)  /experiments/ENCSR864ECD/  Histone ChIP-seq  \n",
       "9   female child (16 years)  /experiments/ENCSR904KDP/  Histone ChIP-seq  \n",
       "10    male adult (60 years)  /experiments/ENCSR737WCC/  Histone ChIP-seq  \n",
       "11  female adult (61 years)  /experiments/ENCSR981USF/  Histone ChIP-seq  \n",
       "12  female adult (61 years)  /experiments/ENCSR211SBE/  Histone ChIP-seq  "
      ]
     },
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    {
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     "text": [
      "\n",
      "Enter the indices of rows to use :  0 1 2 3 4 5 \n"
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    },
    {
     "data": {
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       "      <th>file</th>\n",
       "      <th>dataset</th>\n",
       "      <th>project</th>\n",
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       "      <th>cloud_metadata</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>/files/ENCFF466ADC/</td>\n",
       "      <td>/experiments/ENCSR208WDY/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
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       "      <td>https://encode-public.s3.amazonaws.com/2020/08...</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>/files/ENCFF379BAB/</td>\n",
       "      <td>/experiments/ENCSR368BOE/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
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       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>/files/ENCFF596VKC/</td>\n",
       "      <td>/experiments/ENCSR385YCN/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
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       "      <td>https://encode-public.s3.amazonaws.com/2022/06...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>/files/ENCFF993ISE/</td>\n",
       "      <td>/experiments/ENCSR429VWL/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
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       "      <td>female adult (51 years)</td>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/09...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>/files/ENCFF880VPE/</td>\n",
       "      <td>/experiments/ENCSR788WNE/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>signal p-value</td>\n",
       "      <td>H3K4me3</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (60 years)</td>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>lower lobe of right lung</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2022/06...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>/files/ENCFF074QVI/</td>\n",
       "      <td>/experiments/ENCSR791BWS/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>signal p-value</td>\n",
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       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "                  file                    dataset  project  \\\n",
       "0  /files/ENCFF466ADC/  /experiments/ENCSR208WDY/  ENCODE4   \n",
       "1  /files/ENCFF379BAB/  /experiments/ENCSR368BOE/  ENCODE4   \n",
       "2  /files/ENCFF596VKC/  /experiments/ENCSR385YCN/  ENCODE4   \n",
       "3  /files/ENCFF993ISE/  /experiments/ENCSR429VWL/  ENCODE4   \n",
       "4  /files/ENCFF880VPE/  /experiments/ENCSR788WNE/  ENCODE4   \n",
       "5  /files/ENCFF074QVI/  /experiments/ENCSR791BWS/  ENCODE4   \n",
       "\n",
       "  biological_replicates     output_type   target cell_slims  \\\n",
       "0                   [1]  signal p-value  H3K4me3         []   \n",
       "1                   [1]  signal p-value  H3K4me3         []   \n",
       "2                   [1]  signal p-value  H3K4me3         []   \n",
       "3                   [1]  signal p-value  H3K4me3         []   \n",
       "4                   [1]  signal p-value  H3K4me3         []   \n",
       "5                   [1]  signal p-value  H3K4me3         []   \n",
       "\n",
       "  developmental_slims                  summary organ_slims  \\\n",
       "0          [endoderm]  female adult (53 years)      [lung]   \n",
       "1          [endoderm]    male adult (60 years)      [lung]   \n",
       "2          [endoderm]    male adult (60 years)      [lung]   \n",
       "3          [endoderm]  female adult (51 years)      [lung]   \n",
       "4          [endoderm]    male adult (60 years)      [lung]   \n",
       "5          [endoderm]  female adult (59 years)      [lung]   \n",
       "\n",
       "           system_slims                 term_name  \\\n",
       "0  [respiratory system]   upper lobe of left lung   \n",
       "1  [respiratory system]   lower lobe of left lung   \n",
       "2  [respiratory system]  upper lobe of right lung   \n",
       "3  [respiratory system]   upper lobe of left lung   \n",
       "4  [respiratory system]  lower lobe of right lung   \n",
       "5  [respiratory system]   lower lobe of left lung   \n",
       "\n",
       "                                      cloud_metadata  \n",
       "0  https://encode-public.s3.amazonaws.com/2020/08...  \n",
       "1  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "2  https://encode-public.s3.amazonaws.com/2022/06...  \n",
       "3  https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "4  https://encode-public.s3.amazonaws.com/2022/06...  \n",
       "5  https://encode-public.s3.amazonaws.com/2020/07...  "
      ]
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      "\n",
      "Enter the indices of rows to use :  0 1 2 3 4 5\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://www.encodeproject.org/search/?type=Experiment&status=released&assay_title=TF+ChIP-seq&biosample_ontology.classification=tissue&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&replicates.library.biosample.perturbed=false&searchTerm=lung&award.project=ENCODE&target.label=CTCF&frame=embedded&format=json\n"
     ]
    },
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
       "      <th>term_name</th>\n",
       "      <th>cell_slims</th>\n",
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>[lung]</td>\n",
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       "      <td>upper lobe of right lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
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       "      <td>/experiments/ENCSR164ASX/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
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       "      <td>[]</td>\n",
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       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>lower lobe of left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (60 years)</td>\n",
       "      <td>/experiments/ENCSR195POA/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>[]</td>\n",
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       "      <td>male adult (37 years)</td>\n",
       "      <td>/experiments/ENCSR027FSZ/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>female adult (51 years)</td>\n",
       "      <td>/experiments/ENCSR972LYL/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>female adult (53 years)</td>\n",
       "      <td>/experiments/ENCSR970UZD/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (54 years)</td>\n",
       "      <td>/experiments/ENCSR964BKO/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>lower lobe of left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>female adult (59 years)</td>\n",
       "      <td>/experiments/ENCSR133AFF/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (40 years)</td>\n",
       "      <td>/experiments/ENCSR255SQR/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (54 years)</td>\n",
       "      <td>/experiments/ENCSR463XCZ/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>female adult (53 years)</td>\n",
       "      <td>/experiments/ENCSR224WWI/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>female adult (51 years)</td>\n",
       "      <td>/experiments/ENCSR799TJD/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>left lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>female child (16 years)</td>\n",
       "      <td>/experiments/ENCSR736PZW/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>lung</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (27 years) male adult (35 years)</td>\n",
       "      <td>/experiments/ENCSR000DMH/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>[heart]</td>\n",
       "      <td>[circulatory system]</td>\n",
       "      <td>left ventricle myocardium inferior</td>\n",
       "      <td>[]</td>\n",
       "      <td>[mesoderm]</td>\n",
       "      <td>male adult (60 years)</td>\n",
       "      <td>/experiments/ENCSR068HEE/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>[spleen, immune organ]</td>\n",
       "      <td>[digestive system, immune system]</td>\n",
       "      <td>spleen</td>\n",
       "      <td>[]</td>\n",
       "      <td>[mesoderm]</td>\n",
       "      <td>female adult (61 years)</td>\n",
       "      <td>/experiments/ENCSR466TNQ/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>[pancreas]</td>\n",
       "      <td>[]</td>\n",
       "      <td>pancreas</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>female adult (61 years)</td>\n",
       "      <td>/experiments/ENCSR253ALG/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "               organ_slims                       system_slims  \\\n",
       "0                   [lung]               [respiratory system]   \n",
       "1                   [lung]               [respiratory system]   \n",
       "2                   [lung]               [respiratory system]   \n",
       "3                   [lung]               [respiratory system]   \n",
       "4                   [lung]               [respiratory system]   \n",
       "5                   [lung]               [respiratory system]   \n",
       "6                   [lung]               [respiratory system]   \n",
       "7                   [lung]               [respiratory system]   \n",
       "8                   [lung]               [respiratory system]   \n",
       "9                   [lung]               [respiratory system]   \n",
       "10                  [lung]               [respiratory system]   \n",
       "11                  [lung]               [respiratory system]   \n",
       "12                  [lung]               [respiratory system]   \n",
       "13                  [lung]               [respiratory system]   \n",
       "14                 [heart]               [circulatory system]   \n",
       "15  [spleen, immune organ]  [digestive system, immune system]   \n",
       "16              [pancreas]                                 []   \n",
       "\n",
       "                             term_name cell_slims developmental_slims  \\\n",
       "0             upper lobe of right lung         []          [endoderm]   \n",
       "1             lower lobe of right lung         []          [endoderm]   \n",
       "2              lower lobe of left lung         []          [endoderm]   \n",
       "3              upper lobe of left lung         []          [endoderm]   \n",
       "4              upper lobe of left lung         []          [endoderm]   \n",
       "5              upper lobe of left lung         []          [endoderm]   \n",
       "6              upper lobe of left lung         []          [endoderm]   \n",
       "7              lower lobe of left lung         []          [endoderm]   \n",
       "8                            left lung         []          [endoderm]   \n",
       "9              upper lobe of left lung         []          [endoderm]   \n",
       "10             upper lobe of left lung         []          [endoderm]   \n",
       "11             upper lobe of left lung         []          [endoderm]   \n",
       "12                           left lung         []          [endoderm]   \n",
       "13                                lung         []          [endoderm]   \n",
       "14  left ventricle myocardium inferior         []          [mesoderm]   \n",
       "15                              spleen         []          [mesoderm]   \n",
       "16                            pancreas         []          [endoderm]   \n",
       "\n",
       "                                        summary                    dataset  \\\n",
       "0                         male adult (60 years)  /experiments/ENCSR164ASX/   \n",
       "1                         male adult (60 years)  /experiments/ENCSR863HZM/   \n",
       "2                         male adult (60 years)  /experiments/ENCSR195POA/   \n",
       "3                         male adult (37 years)  /experiments/ENCSR027FSZ/   \n",
       "4                       female adult (51 years)  /experiments/ENCSR972LYL/   \n",
       "5                       female adult (53 years)  /experiments/ENCSR970UZD/   \n",
       "6                         male adult (54 years)  /experiments/ENCSR964BKO/   \n",
       "7                       female adult (59 years)  /experiments/ENCSR133AFF/   \n",
       "8                         male adult (40 years)  /experiments/ENCSR255SQR/   \n",
       "9                         male adult (54 years)  /experiments/ENCSR463XCZ/   \n",
       "10                      female adult (53 years)  /experiments/ENCSR224WWI/   \n",
       "11                      female adult (51 years)  /experiments/ENCSR799TJD/   \n",
       "12                      female child (16 years)  /experiments/ENCSR736PZW/   \n",
       "13  male adult (27 years) male adult (35 years)  /experiments/ENCSR000DMH/   \n",
       "14                        male adult (60 years)  /experiments/ENCSR068HEE/   \n",
       "15                      female adult (61 years)  /experiments/ENCSR466TNQ/   \n",
       "16                      female adult (61 years)  /experiments/ENCSR253ALG/   \n",
       "\n",
       "          assay  \n",
       "0   TF ChIP-seq  \n",
       "1   TF ChIP-seq  \n",
       "2   TF ChIP-seq  \n",
       "3   TF ChIP-seq  \n",
       "4   TF ChIP-seq  \n",
       "5   TF ChIP-seq  \n",
       "6   TF ChIP-seq  \n",
       "7   TF ChIP-seq  \n",
       "8   TF ChIP-seq  \n",
       "9   TF ChIP-seq  \n",
       "10  TF ChIP-seq  \n",
       "11  TF ChIP-seq  \n",
       "12  TF ChIP-seq  \n",
       "13  TF ChIP-seq  \n",
       "14  TF ChIP-seq  \n",
       "15  TF ChIP-seq  \n",
       "16  TF ChIP-seq  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "\n",
      "Enter the indices of rows to use :  0 1 2 3 4 5\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>file</th>\n",
       "      <th>dataset</th>\n",
       "      <th>project</th>\n",
       "      <th>biological_replicates</th>\n",
       "      <th>output_type</th>\n",
       "      <th>target</th>\n",
       "      <th>cell_slims</th>\n",
       "      <th>developmental_slims</th>\n",
       "      <th>summary</th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
       "      <th>term_name</th>\n",
       "      <th>cloud_metadata</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>/files/ENCFF354FKN/</td>\n",
       "      <td>/experiments/ENCSR027FSZ/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>IDR thresholded peaks</td>\n",
       "      <td>CTCF</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (37 years)</td>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/08...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>/files/ENCFF238PEB/</td>\n",
       "      <td>/experiments/ENCSR164ASX/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>IDR thresholded peaks</td>\n",
       "      <td>CTCF</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (60 years)</td>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of right lung</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2022/06...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>/files/ENCFF711KWX/</td>\n",
       "      <td>/experiments/ENCSR195POA/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>IDR thresholded peaks</td>\n",
       "      <td>CTCF</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (60 years)</td>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>lower lobe of left lung</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>/files/ENCFF183WDD/</td>\n",
       "      <td>/experiments/ENCSR863HZM/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>IDR thresholded peaks</td>\n",
       "      <td>CTCF</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>male adult (60 years)</td>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>lower lobe of right lung</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2022/06...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>/files/ENCFF786YIA/</td>\n",
       "      <td>/experiments/ENCSR970UZD/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>IDR thresholded peaks</td>\n",
       "      <td>CTCF</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>female adult (53 years)</td>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/08...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>/files/ENCFF647HXE/</td>\n",
       "      <td>/experiments/ENCSR972LYL/</td>\n",
       "      <td>ENCODE4</td>\n",
       "      <td>[1]</td>\n",
       "      <td>IDR thresholded peaks</td>\n",
       "      <td>CTCF</td>\n",
       "      <td>[]</td>\n",
       "      <td>[endoderm]</td>\n",
       "      <td>female adult (51 years)</td>\n",
       "      <td>[lung]</td>\n",
       "      <td>[respiratory system]</td>\n",
       "      <td>upper lobe of left lung</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/08...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                  file                    dataset  project  \\\n",
       "0  /files/ENCFF354FKN/  /experiments/ENCSR027FSZ/  ENCODE4   \n",
       "1  /files/ENCFF238PEB/  /experiments/ENCSR164ASX/  ENCODE4   \n",
       "2  /files/ENCFF711KWX/  /experiments/ENCSR195POA/  ENCODE4   \n",
       "3  /files/ENCFF183WDD/  /experiments/ENCSR863HZM/  ENCODE4   \n",
       "4  /files/ENCFF786YIA/  /experiments/ENCSR970UZD/  ENCODE4   \n",
       "5  /files/ENCFF647HXE/  /experiments/ENCSR972LYL/  ENCODE4   \n",
       "\n",
       "  biological_replicates            output_type target cell_slims  \\\n",
       "0                   [1]  IDR thresholded peaks   CTCF         []   \n",
       "1                   [1]  IDR thresholded peaks   CTCF         []   \n",
       "2                   [1]  IDR thresholded peaks   CTCF         []   \n",
       "3                   [1]  IDR thresholded peaks   CTCF         []   \n",
       "4                   [1]  IDR thresholded peaks   CTCF         []   \n",
       "5                   [1]  IDR thresholded peaks   CTCF         []   \n",
       "\n",
       "  developmental_slims                  summary organ_slims  \\\n",
       "0          [endoderm]    male adult (37 years)      [lung]   \n",
       "1          [endoderm]    male adult (60 years)      [lung]   \n",
       "2          [endoderm]    male adult (60 years)      [lung]   \n",
       "3          [endoderm]    male adult (60 years)      [lung]   \n",
       "4          [endoderm]  female adult (53 years)      [lung]   \n",
       "5          [endoderm]  female adult (51 years)      [lung]   \n",
       "\n",
       "           system_slims                 term_name  \\\n",
       "0  [respiratory system]   upper lobe of left lung   \n",
       "1  [respiratory system]  upper lobe of right lung   \n",
       "2  [respiratory system]   lower lobe of left lung   \n",
       "3  [respiratory system]  lower lobe of right lung   \n",
       "4  [respiratory system]   upper lobe of left lung   \n",
       "5  [respiratory system]   upper lobe of left lung   \n",
       "\n",
       "                                      cloud_metadata  \n",
       "0  https://encode-public.s3.amazonaws.com/2020/08...  \n",
       "1  https://encode-public.s3.amazonaws.com/2022/06...  \n",
       "2  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "3  https://encode-public.s3.amazonaws.com/2022/06...  \n",
       "4  https://encode-public.s3.amazonaws.com/2020/08...  \n",
       "5  https://encode-public.s3.amazonaws.com/2020/08...  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "\n",
      "Enter the indices of rows to use :  0 1 2 3 4 5\n"
     ]
    }
   ],
   "source": [
    "results4 = c4.parse_url()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 127,
   "id": "c992b461-1a46-4ba2-8748-623b3aa1dcb6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "defaultdict(list,\n",
       "            {'H3K4me3': ['https://encode-public.s3.amazonaws.com/2020/08/14/16ad20c8-3eec-438e-b436-15606ab9ff9d/ENCFF466ADC.bigWig',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/07/23/fc04133a-1d99-4a7d-b53b-3f0df6bdbbf8/ENCFF379BAB.bigWig',\n",
       "              'https://encode-public.s3.amazonaws.com/2022/06/06/a7a8fa51-d43a-4b7c-a3b3-ca08c35cdeca/ENCFF596VKC.bigWig',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/09/23/42d2781e-5908-4186-bb71-fcd9139a3807/ENCFF993ISE.bigWig',\n",
       "              'https://encode-public.s3.amazonaws.com/2022/06/06/ef6e6374-6329-4deb-8efd-ac1282c28e41/ENCFF880VPE.bigWig',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/07/23/41bd3a68-fe93-48ec-a5f7-25281c849d13/ENCFF074QVI.bigWig'],\n",
       "             'CTCF': ['https://encode-public.s3.amazonaws.com/2020/08/13/592aee4a-97fc-47ae-afac-895374f45029/ENCFF354FKN.bed.gz',\n",
       "              'https://encode-public.s3.amazonaws.com/2022/06/06/26042892-2860-4018-8197-7323807dcae5/ENCFF238PEB.bed.gz',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/07/09/e85b0dd4-860c-4650-b7c4-8e4901e13ecb/ENCFF711KWX.bed.gz',\n",
       "              'https://encode-public.s3.amazonaws.com/2022/06/06/f4763cfe-7fc8-45cd-a585-aad7ddcb0224/ENCFF183WDD.bed.gz',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/08/13/12866b03-3de4-4104-acc2-9124105adb3c/ENCFF786YIA.bed.gz',\n",
       "              'https://encode-public.s3.amazonaws.com/2020/08/13/51d897da-470a-4db4-98a1-97400ae28ea8/ENCFF647HXE.bed.gz']})"
      ]
     },
     "execution_count": 127,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "results4"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "da287b99-54ff-4289-9056-e6ed301b362f",
   "metadata": {},
   "source": [
    "#### To change genome build to hg19 (default is GRCh38):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 137,
   "id": "cf2fa56e-d9c0-47d7-8e09-069d4676ebce",
   "metadata": {},
   "outputs": [],
   "source": [
    "c5 = encode.FeatureConfig('ovary',  False, False, \"H3K4me3\", \"CTCF\", )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 138,
   "id": "15298957-a92b-4e72-a2f0-facfa1b1939b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://www.encodeproject.org/search/?type=Experiment&status=released&assay_title=Histone+ChIP-seq&biosample_ontology.classification=tissue&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&replicates.library.biosample.perturbed=false&searchTerm=ovary&award.project=ENCODE&target.label=H3K4me3&frame=embedded&format=json\n"
     ]
    },
    {
     "data": {
      "text/html": [
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       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
       "      <th>term_name</th>\n",
       "      <th>cell_slims</th>\n",
       "      <th>developmental_slims</th>\n",
       "      <th>summary</th>\n",
       "      <th>dataset</th>\n",
       "      <th>assay</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>[ovary, gonad]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>ovary</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (53 years)</td>\n",
       "      <td>/experiments/ENCSR828CCQ/</td>\n",
       "      <td>Histone ChIP-seq</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      organ_slims           system_slims term_name cell_slims  \\\n",
       "0  [ovary, gonad]  [reproductive system]     ovary         []   \n",
       "\n",
       "  developmental_slims                  summary                    dataset  \\\n",
       "0                  []  female adult (53 years)  /experiments/ENCSR828CCQ/   \n",
       "\n",
       "              assay  \n",
       "0  Histone ChIP-seq  "
      ]
     },
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    },
    {
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     "data": {
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       "      <td>[]</td>\n",
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      ],
      "text/plain": [
       "                  file                    dataset  project  \\\n",
       "0  /files/ENCFF333NHP/  /experiments/ENCSR828CCQ/  ENCODE3   \n",
       "\n",
       "  biological_replicates     output_type   target cell_slims  \\\n",
       "0                   [1]  signal p-value  H3K4me3         []   \n",
       "\n",
       "  developmental_slims                  summary     organ_slims  \\\n",
       "0                  []  female adult (53 years)  [ovary, gonad]   \n",
       "\n",
       "            system_slims term_name  \\\n",
       "0  [reproductive system]     ovary   \n",
       "\n",
       "                                      cloud_metadata  \n",
       "0  https://encode-public.s3.amazonaws.com/2019/02...  "
      ]
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      "\n",
      "Enter the indices of rows to use :  0\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://www.encodeproject.org/search/?type=Experiment&status=released&assay_title=TF+ChIP-seq&biosample_ontology.classification=tissue&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&replicates.library.biosample.perturbed=false&searchTerm=ovary&award.project=ENCODE&target.label=CTCF&frame=embedded&format=json\n"
     ]
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       "  <thead>\n",
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       "      <th></th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
       "      <th>term_name</th>\n",
       "      <th>cell_slims</th>\n",
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       "      <td>[ovary, gonad]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>ovary</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (41 years)</td>\n",
       "      <td>/experiments/ENCSR934GQS/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      organ_slims           system_slims term_name cell_slims  \\\n",
       "0  [ovary, gonad]  [reproductive system]     ovary         []   \n",
       "1  [ovary, gonad]  [reproductive system]     ovary         []   \n",
       "2  [ovary, gonad]  [reproductive system]     ovary         []   \n",
       "\n",
       "  developmental_slims                  summary                    dataset  \\\n",
       "0                  []  female adult (53 years)  /experiments/ENCSR493APD/   \n",
       "1                  []  female adult (51 years)  /experiments/ENCSR548DDS/   \n",
       "2                  []  female adult (41 years)  /experiments/ENCSR934GQS/   \n",
       "\n",
       "         assay  \n",
       "0  TF ChIP-seq  \n",
       "1  TF ChIP-seq  \n",
       "2  TF ChIP-seq  "
      ]
     },
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    },
    {
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     "text": [
      "\n",
      "Enter the indices of rows to use :  0 1 2\n"
     ]
    },
    {
     "data": {
      "text/html": [
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       "  <tbody>\n",
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       "      <th>0</th>\n",
       "      <td>/files/ENCFF261BWI/</td>\n",
       "      <td>/experiments/ENCSR493APD/</td>\n",
       "      <td>ENCODE3</td>\n",
       "      <td>[1]</td>\n",
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       "      <td>CTCF</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
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       "      <td>[ovary, gonad]</td>\n",
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       "      <td>https://encode-public.s3.amazonaws.com/2017/08...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>/files/ENCFF237NQY/</td>\n",
       "      <td>/experiments/ENCSR493APD/</td>\n",
       "      <td>ENCODE3</td>\n",
       "      <td>[1]</td>\n",
       "      <td>peaks and background as input for IDR</td>\n",
       "      <td>CTCF</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (53 years)</td>\n",
       "      <td>[ovary, gonad]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>ovary</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/08...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>/files/ENCFF522DLJ/</td>\n",
       "      <td>/experiments/ENCSR548DDS/</td>\n",
       "      <td>ENCODE3</td>\n",
       "      <td>[1]</td>\n",
       "      <td>pseudoreplicated IDR thresholded peaks</td>\n",
       "      <td>CTCF</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (51 years)</td>\n",
       "      <td>[ovary, gonad]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>ovary</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/08...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>/files/ENCFF333FVM/</td>\n",
       "      <td>/experiments/ENCSR548DDS/</td>\n",
       "      <td>ENCODE3</td>\n",
       "      <td>[1]</td>\n",
       "      <td>peaks and background as input for IDR</td>\n",
       "      <td>CTCF</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (51 years)</td>\n",
       "      <td>[ovary, gonad]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>ovary</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/08...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                  file                    dataset  project  \\\n",
       "0  /files/ENCFF261BWI/  /experiments/ENCSR493APD/  ENCODE3   \n",
       "1  /files/ENCFF237NQY/  /experiments/ENCSR493APD/  ENCODE3   \n",
       "2  /files/ENCFF522DLJ/  /experiments/ENCSR548DDS/  ENCODE3   \n",
       "3  /files/ENCFF333FVM/  /experiments/ENCSR548DDS/  ENCODE3   \n",
       "\n",
       "  biological_replicates                             output_type target  \\\n",
       "0                   [1]  pseudoreplicated IDR thresholded peaks   CTCF   \n",
       "1                   [1]   peaks and background as input for IDR   CTCF   \n",
       "2                   [1]  pseudoreplicated IDR thresholded peaks   CTCF   \n",
       "3                   [1]   peaks and background as input for IDR   CTCF   \n",
       "\n",
       "  cell_slims developmental_slims                  summary     organ_slims  \\\n",
       "0         []                  []  female adult (53 years)  [ovary, gonad]   \n",
       "1         []                  []  female adult (53 years)  [ovary, gonad]   \n",
       "2         []                  []  female adult (51 years)  [ovary, gonad]   \n",
       "3         []                  []  female adult (51 years)  [ovary, gonad]   \n",
       "\n",
       "            system_slims term_name  \\\n",
       "0  [reproductive system]     ovary   \n",
       "1  [reproductive system]     ovary   \n",
       "2  [reproductive system]     ovary   \n",
       "3  [reproductive system]     ovary   \n",
       "\n",
       "                                      cloud_metadata  \n",
       "0  https://encode-public.s3.amazonaws.com/2017/08...  \n",
       "1  https://encode-public.s3.amazonaws.com/2017/08...  \n",
       "2  https://encode-public.s3.amazonaws.com/2017/08...  \n",
       "3  https://encode-public.s3.amazonaws.com/2017/08...  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "\n",
      "Enter the indices of rows to use :  0 2\n"
     ]
    }
   ],
   "source": [
    "results5 = c5.parse_url(genome_build='hg19')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 139,
   "id": "498f429f-3714-4664-9e63-b008f7b29ba9",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "defaultdict(list,\n",
       "            {'H3K4me3': ['https://encode-public.s3.amazonaws.com/2019/02/11/4f5bd7b5-8478-44ab-8858-3eb0971e44f5/ENCFF333NHP.bigWig'],\n",
       "             'CTCF': ['https://encode-public.s3.amazonaws.com/2017/08/11/5cc16585-e173-48f6-8299-f0d6d9a27658/ENCFF261BWI.bed.gz',\n",
       "              'https://encode-public.s3.amazonaws.com/2017/08/11/09c88ed4-590d-45e0-b90c-cd085e06d826/ENCFF522DLJ.bed.gz']})"
      ]
     },
     "execution_count": 139,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "results5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "8b32a3d4-ad71-47fe-9587-975c566ad27f",
   "metadata": {},
   "outputs": [],
   "source": [
    "c6 = encode.FeatureConfig('ovary',  False, False, \"DNase\", \"POLR2A\", )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "21bfab3f-dcd3-43cb-a672-4575256f0370",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://www.encodeproject.org/search/?type=Experiment&status=released&assay_title=DNase-seq&biosample_ontology.classification=tissue&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&replicates.library.biosample.perturbed=false&searchTerm=ovary&award.project=ENCODE&frame=embedded&format=json\n"
     ]
    },
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
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       "      <td>/experiments/ENCSR330ZBO/</td>\n",
       "      <td>DNase-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>[ovary, gonad]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>ovary</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (47 years)</td>\n",
       "      <td>/experiments/ENCSR732RIC/</td>\n",
       "      <td>DNase-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>[ovary, gonad]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>ovary</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (41 years)</td>\n",
       "      <td>/experiments/ENCSR872DUY/</td>\n",
       "      <td>DNase-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>[gonad, ovary]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>ovary</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (46 years)</td>\n",
       "      <td>/experiments/ENCSR798XLO/</td>\n",
       "      <td>DNase-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>[ovary, gonad]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>ovary</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (61 years)</td>\n",
       "      <td>/experiments/ENCSR138UGH/</td>\n",
       "      <td>DNase-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>[ovary, gonad]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>ovary</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (53 years)</td>\n",
       "      <td>/experiments/ENCSR930PDT/</td>\n",
       "      <td>DNase-seq</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>[gonad, ovary]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>ovary</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (51 years)</td>\n",
       "      <td>/experiments/ENCSR365NDK/</td>\n",
       "      <td>DNase-seq</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      organ_slims           system_slims term_name cell_slims  \\\n",
       "0  [ovary, gonad]  [reproductive system]     ovary         []   \n",
       "1  [ovary, gonad]  [reproductive system]     ovary         []   \n",
       "2  [ovary, gonad]  [reproductive system]     ovary         []   \n",
       "3  [gonad, ovary]  [reproductive system]     ovary         []   \n",
       "4  [ovary, gonad]  [reproductive system]     ovary         []   \n",
       "5  [ovary, gonad]  [reproductive system]     ovary         []   \n",
       "6  [gonad, ovary]  [reproductive system]     ovary         []   \n",
       "\n",
       "  developmental_slims                  summary                    dataset  \\\n",
       "0                  []  female adult (59 years)  /experiments/ENCSR330ZBO/   \n",
       "1                  []  female adult (47 years)  /experiments/ENCSR732RIC/   \n",
       "2                  []  female adult (41 years)  /experiments/ENCSR872DUY/   \n",
       "3                  []  female adult (46 years)  /experiments/ENCSR798XLO/   \n",
       "4                  []  female adult (61 years)  /experiments/ENCSR138UGH/   \n",
       "5                  []  female adult (53 years)  /experiments/ENCSR930PDT/   \n",
       "6                  []  female adult (51 years)  /experiments/ENCSR365NDK/   \n",
       "\n",
       "       assay  \n",
       "0  DNase-seq  \n",
       "1  DNase-seq  \n",
       "2  DNase-seq  \n",
       "3  DNase-seq  \n",
       "4  DNase-seq  \n",
       "5  DNase-seq  \n",
       "6  DNase-seq  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "\n",
      "Enter the indices of rows to use :  0 1 2 3 4 5 6\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "No matched files found\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://www.encodeproject.org/search/?type=Experiment&status=released&assay_title=TF+ChIP-seq&biosample_ontology.classification=tissue&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&replicates.library.biosample.perturbed=false&searchTerm=ovary&award.project=ENCODE&target.label=POLR2A&frame=embedded&format=json\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
       "      <th>term_name</th>\n",
       "      <th>cell_slims</th>\n",
       "      <th>developmental_slims</th>\n",
       "      <th>summary</th>\n",
       "      <th>dataset</th>\n",
       "      <th>assay</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>[ovary, gonad]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>ovary</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (53 years)</td>\n",
       "      <td>/experiments/ENCSR754DWU/</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      organ_slims           system_slims term_name cell_slims  \\\n",
       "0  [ovary, gonad]  [reproductive system]     ovary         []   \n",
       "\n",
       "  developmental_slims                  summary                    dataset  \\\n",
       "0                  []  female adult (53 years)  /experiments/ENCSR754DWU/   \n",
       "\n",
       "         assay  \n",
       "0  TF ChIP-seq  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "\n",
      "Enter the indices of rows to use :  0\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>file</th>\n",
       "      <th>dataset</th>\n",
       "      <th>project</th>\n",
       "      <th>biological_replicates</th>\n",
       "      <th>output_type</th>\n",
       "      <th>target</th>\n",
       "      <th>cell_slims</th>\n",
       "      <th>developmental_slims</th>\n",
       "      <th>summary</th>\n",
       "      <th>organ_slims</th>\n",
       "      <th>system_slims</th>\n",
       "      <th>term_name</th>\n",
       "      <th>cloud_metadata</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>/files/ENCFF077ESE/</td>\n",
       "      <td>/experiments/ENCSR754DWU/</td>\n",
       "      <td>ENCODE3</td>\n",
       "      <td>[1]</td>\n",
       "      <td>signal p-value</td>\n",
       "      <td>POLR2A</td>\n",
       "      <td>[]</td>\n",
       "      <td>[]</td>\n",
       "      <td>female adult (53 years)</td>\n",
       "      <td>[ovary, gonad]</td>\n",
       "      <td>[reproductive system]</td>\n",
       "      <td>ovary</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/08...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                  file                    dataset  project  \\\n",
       "0  /files/ENCFF077ESE/  /experiments/ENCSR754DWU/  ENCODE3   \n",
       "\n",
       "  biological_replicates     output_type  target cell_slims  \\\n",
       "0                   [1]  signal p-value  POLR2A         []   \n",
       "\n",
       "  developmental_slims                  summary     organ_slims  \\\n",
       "0                  []  female adult (53 years)  [ovary, gonad]   \n",
       "\n",
       "            system_slims term_name  \\\n",
       "0  [reproductive system]     ovary   \n",
       "\n",
       "                                      cloud_metadata  \n",
       "0  https://encode-public.s3.amazonaws.com/2017/08...  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "\n",
      "Enter the indices of rows to use :  0\n"
     ]
    }
   ],
   "source": [
    "results6 = c6.parse_url(genome_build='hg19') # No matched files found for DNase becaue all biomsample datasets don't have hg19 ref genome build entries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c14f9299-cd70-4c3d-be04-eb77e610a06d",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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