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alimanfoo/agamp4-reference-examples.ipynb

Created November 9, 2020 10:58
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agamp4-reference-examples.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# AgamP4 resource in GCS\n",
"\n",
"A quick guide to accessing AgamP4 reference genome and genome annotations on GCS."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Reference genome - read from GCS\n",
"\n",
"The reference genome is available in zarr format and can be read directly from GCS..."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import zarr\n",
"import fsspec"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"<zarr.hierarchy.Group '/'>"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"genome_path_gcs = 'gs://vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.zarr'\n",
"genome_store = fsspec.get_mapper(genome_path_gcs)\n",
"genome = zarr.open_consolidated(genome_store)\n",
"genome"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"/\n",
" ├── 2L (49364325,) |S1\n",
" ├── 2R (61545105,) |S1\n",
" ├── 3L (41963435,) |S1\n",
" ├── 3R (53200684,) |S1\n",
" ├── Mt (15363,) |S1\n",
" ├── UNKN (42389979,) |S1\n",
" ├── X (24393108,) |S1\n",
" └── Y_unplaced (237045,) |S1\n"
]
}
],
"source": [
"print(genome.tree())"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"49364325"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"len(genome['2L'])"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"<zarr.core.Array '/2L' (49364325,) |S1>"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"genome['2L']"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([b'a', b'a', b'c', ..., b'a', b'a', b'a'], dtype='|S1')"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"seq = genome['2L'][:]\n",
"seq"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Reference genome - local download\n",
"\n",
"You can also download the reference genome locally if you prefer..."
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"--2020-11-09 10:57:01-- https://storage.googleapis.com/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.gz\n",
"Resolving storage.googleapis.com (storage.googleapis.com)... 64.233.191.128, 173.194.192.128, 209.85.146.128, ...\n",
"Connecting to storage.googleapis.com (storage.googleapis.com)|64.233.191.128|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 80872688 (77M) [application/gzip]\n",
"Saving to: ‘Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.gz’\n",
"\n",
"Anopheles-gambiae-P 100%[===================>] 77.13M 111MB/s in 0.7s \n",
"\n",
"2020-11-09 10:57:02 (111 MB/s) - ‘Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.gz’ saved [80872688/80872688]\n",
"\n"
]
}
],
"source": [
"!wget --no-clobber https://storage.googleapis.com/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.gz"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"!gunzip Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.gz"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"import pyfasta"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"<pyfasta.fasta.Fasta at 0x7f269a72d750>"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# don't forget the key_fn argument\n",
"genome = pyfasta.Fasta('Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa', key_fn=lambda x: x.split()[0])\n",
"genome"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Genome annotations - read from GCS\n",
"\n",
"Genome annotations (last version produced before vectorbase migrated to eupathdb) can be read directly from GCS via petl..."
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"import petl as etl\n",
"import petlx"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"geneset_path_gcs = 'gs://vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.12.gff3.gz'"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table class='petl'>\n",
"<thead>\n",
"<tr>\n",
"<th>seqid</th>\n",
"<th>source</th>\n",
"<th>type</th>\n",
"<th>start</th>\n",
"<th>end</th>\n",
"<th>score</th>\n",
"<th>strand</th>\n",
"<th>phase</th>\n",
"<th>attributes</th>\n",
"</tr>\n",
"</thead>\n",
"<tbody>\n",
"<tr>\n",
"<td>2L</td>\n",
"<td>VectorBase</td>\n",
"<td>chromosome</td>\n",
"<td style='text-align: right'>1</td>\n",
"<td style='text-align: right'>49364325</td>\n",
"<td>.</td>\n",
"<td>.</td>\n",
"<td>.</td>\n",
"<td>{'ID': '2L', 'Alias': 'CM000356.1'}</td>\n",
"</tr>\n",
"<tr>\n",
"<td>2L</td>\n",
"<td>VectorBase</td>\n",
"<td>gene</td>\n",
"<td style='text-align: right'>157348</td>\n",
"<td style='text-align: right'>186936</td>\n",
"<td>.</td>\n",
"<td>-</td>\n",
"<td>.</td>\n",
"<td>{'ID': 'AGAP004677', 'biotype': 'protein_coding', 'description': 'methylenetetrahydrofolate dehydrogenase(NAD ) / 5,10-methenyltetrahydrofolate [Source:VB Community Annotation]', 'version': '1'}</td>\n",
"</tr>\n",
"<tr>\n",
"<td>2L</td>\n",
"<td>VectorBase</td>\n",
"<td>mRNA</td>\n",
"<td style='text-align: right'>157348</td>\n",
"<td style='text-align: right'>181305</td>\n",
"<td>.</td>\n",
"<td>-</td>\n",
"<td>.</td>\n",
"<td>{'ID': 'AGAP004677-RA', 'Parent': 'AGAP004677', 'Dbxref': 'Celera_Pep:agCP1943,KEGG_Enzyme:00670 1.5.1.5 3.5.4.9,KEGG_Enzyme:00720 1.5.1.5 3.5.4.9,RefSeq:XM_001687731.1,RefSeq:XP_001687783.1,STRING:7165.AGAP004677-PA,UniParc:UPI0000020060,UniProtKB:A7UTF7,NCBI_GP:EDO64016.1', 'Ontology_term': 'GO:0003824,GO:0004477,GO:0004487,GO:0004488,GO:0035999,GO:0046653,GO:0055114', 'biotype': 'protein_coding', 'version': '1'}</td>\n",
"</tr>\n",
"<tr>\n",
"<td>2L</td>\n",
"<td>VectorBase</td>\n",
"<td>three_prime_UTR</td>\n",
"<td style='text-align: right'>157348</td>\n",
"<td style='text-align: right'>157495</td>\n",
"<td>.</td>\n",
"<td>-</td>\n",
"<td>.</td>\n",
"<td>{'Parent': 'AGAP004677-RA'}</td>\n",
"</tr>\n",
"<tr>\n",
"<td>2L</td>\n",
"<td>VectorBase</td>\n",
"<td>exon</td>\n",
"<td style='text-align: right'>157348</td>\n",
"<td style='text-align: right'>157623</td>\n",
"<td>.</td>\n",
"<td>-</td>\n",
"<td>.</td>\n",
"<td>{'Parent': 'AGAP004677-RA', 'Name': 'AGAP004677-RB-E4', 'constitutive': '1', 'rank': '4'}</td>\n",
"</tr>\n",
"</tbody>\n",
"</table>\n",
"<p><strong>...</strong></p>"
],
"text/plain": [
"+-------+--------------+-------------------+--------+----------+-------+--------+-------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
"| seqid | source | type | start | end | score | strand | phase | attributes |\n",
"+=======+==============+===================+========+==========+=======+========+=======+====================================================================================================================================================================================================================================================================================================================================================================================================================================+\n",
"| '2L' | 'VectorBase' | 'chromosome' | 1 | 49364325 | '.' | '.' | '.' | {'ID': '2L', 'Alias': 'CM000356.1'} |\n",
"+-------+--------------+-------------------+--------+----------+-------+--------+-------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
"| '2L' | 'VectorBase' | 'gene' | 157348 | 186936 | '.' | '-' | '.' | {'ID': 'AGAP004677', 'biotype': 'protein_coding', 'description': 'methylenetetrahydrofolate dehydrogenase(NAD ) / 5,10-methenyltetrahydrofolate [Source:VB Community Annotation]', 'version': '1'} |\n",
"+-------+--------------+-------------------+--------+----------+-------+--------+-------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
"| '2L' | 'VectorBase' | 'mRNA' | 157348 | 181305 | '.' | '-' | '.' | {'ID': 'AGAP004677-RA', 'Parent': 'AGAP004677', 'Dbxref': 'Celera_Pep:agCP1943,KEGG_Enzyme:00670 1.5.1.5 3.5.4.9,KEGG_Enzyme:00720 1.5.1.5 3.5.4.9,RefSeq:XM_001687731.1,RefSeq:XP_001687783.1,STRING:7165.AGAP004677-PA,UniParc:UPI0000020060,UniProtKB:A7UTF7,NCBI_GP:EDO64016.1', 'Ontology_term': 'GO:0003824,GO:0004477,GO:0004487,GO:0004488,GO:0035999,GO:0046653,GO:0055114', 'biotype': 'protein_coding', 'version': '1'} |\n",
"+-------+--------------+-------------------+--------+----------+-------+--------+-------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
"| '2L' | 'VectorBase' | 'three_prime_UTR' | 157348 | 157495 | '.' | '-' | '.' | {'Parent': 'AGAP004677-RA'} |\n",
"+-------+--------------+-------------------+--------+----------+-------+--------+-------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
"| '2L' | 'VectorBase' | 'exon' | 157348 | 157623 | '.' | '-' | '.' | {'Parent': 'AGAP004677-RA', 'Name': 'AGAP004677-RB-E4', 'constitutive': '1', 'rank': '4'} |\n",
"+-------+--------------+-------------------+--------+----------+-------+--------+-------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
"..."
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"tbl_geneset = etl.fromgff3(geneset_path_gcs)\n",
"tbl_geneset"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"If you prefer to use pandas, here's how to make a dataframe..."
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"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>seqid</th>\n",
" <th>source</th>\n",
" <th>type</th>\n",
" <th>start</th>\n",
" <th>end</th>\n",
" <th>score</th>\n",
" <th>strand</th>\n",
" <th>phase</th>\n",
" <th>ID</th>\n",
" <th>Name</th>\n",
" <th>Parent</th>\n",
" <th>biotype</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>2L</td>\n",
" <td>VectorBase</td>\n",
" <td>chromosome</td>\n",
" <td>1</td>\n",
" <td>49364325</td>\n",
" <td>.</td>\n",
" <td>.</td>\n",
" <td>.</td>\n",
" <td>2L</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>2L</td>\n",
" <td>VectorBase</td>\n",
" <td>gene</td>\n",
" <td>157348</td>\n",
" <td>186936</td>\n",
" <td>.</td>\n",
" <td>-</td>\n",
" <td>.</td>\n",
" <td>AGAP004677</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>protein_coding</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>2L</td>\n",
" <td>VectorBase</td>\n",
" <td>mRNA</td>\n",
" <td>157348</td>\n",
" <td>181305</td>\n",
" <td>.</td>\n",
" <td>-</td>\n",
" <td>.</td>\n",
" <td>AGAP004677-RA</td>\n",
" <td>None</td>\n",
" <td>AGAP004677</td>\n",
" <td>protein_coding</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>2L</td>\n",
" <td>VectorBase</td>\n",
" <td>three_prime_UTR</td>\n",
" <td>157348</td>\n",
" <td>157495</td>\n",
" <td>.</td>\n",
" <td>-</td>\n",
" <td>.</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>AGAP004677-RA</td>\n",
" <td>None</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>2L</td>\n",
" <td>VectorBase</td>\n",
" <td>exon</td>\n",
" <td>157348</td>\n",
" <td>157623</td>\n",
" <td>.</td>\n",
" <td>-</td>\n",
" <td>.</td>\n",
" <td>None</td>\n",
" <td>AGAP004677-RB-E4</td>\n",
" <td>AGAP004677-RA</td>\n",
" <td>None</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" seqid source type start end score strand phase \\\n",
"0 2L VectorBase chromosome 1 49364325 . . . \n",
"1 2L VectorBase gene 157348 186936 . - . \n",
"2 2L VectorBase mRNA 157348 181305 . - . \n",
"3 2L VectorBase three_prime_UTR 157348 157495 . - . \n",
"4 2L VectorBase exon 157348 157623 . - . \n",
"\n",
" ID Name Parent biotype \n",
"0 2L None None None \n",
"1 AGAP004677 None None protein_coding \n",
"2 AGAP004677-RA None AGAP004677 protein_coding \n",
"3 None None AGAP004677-RA None \n",
"4 None AGAP004677-RB-E4 AGAP004677-RA None "
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df_geneset = (\n",
" tbl_geneset\n",
" # choose the attributes you want to include as columns\n",
" .unpackdict('attributes', ['ID', 'Name', 'Parent', 'biotype'])\n",
" .todataframe()\n",
")\n",
"df_geneset.head()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Note that scikit-allel has a `gff3_to_dataframe` function, but this does not support reading directly from cloud at the moment (PR welcome)."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Genome annotations - local download"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"--2020-11-09 10:57:42-- https://storage.googleapis.com/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.12.gff3.gz\n",
"Resolving storage.googleapis.com (storage.googleapis.com)... 173.194.194.128, 64.233.191.128, 142.250.125.128, ...\n",
"Connecting to storage.googleapis.com (storage.googleapis.com)|173.194.194.128|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 2724130 (2.6M) [application/gzip]\n",
"Saving to: ‘Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.12.gff3.gz’\n",
"\n",
"Anopheles-gambiae-P 100%[===================>] 2.60M --.-KB/s in 0.02s \n",
"\n",
"2020-11-09 10:57:42 (158 MB/s) - ‘Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.12.gff3.gz’ saved [2724130/2724130]\n",
"\n"
]
}
],
"source": [
"!wget --no-clobber https://storage.googleapis.com/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.12.gff3.gz"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [],
"source": [
"import allel"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"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>seqid</th>\n",
" <th>source</th>\n",
" <th>type</th>\n",
" <th>start</th>\n",
" <th>end</th>\n",
" <th>score</th>\n",
" <th>strand</th>\n",
" <th>phase</th>\n",
" <th>ID</th>\n",
" <th>Name</th>\n",
" <th>Parent</th>\n",
" <th>biotype</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>2L</td>\n",
" <td>VectorBase</td>\n",
" <td>chromosome</td>\n",
" <td>1</td>\n",
" <td>49364325</td>\n",
" <td>-1</td>\n",
" <td>.</td>\n",
" <td>-1</td>\n",
" <td>2L</td>\n",
" <td>.</td>\n",
" <td>.</td>\n",
" <td>.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>2L</td>\n",
" <td>VectorBase</td>\n",
" <td>gene</td>\n",
" <td>157348</td>\n",
" <td>186936</td>\n",
" <td>-1</td>\n",
" <td>-</td>\n",
" <td>-1</td>\n",
" <td>AGAP004677</td>\n",
" <td>.</td>\n",
" <td>.</td>\n",
" <td>protein_coding</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>2L</td>\n",
" <td>VectorBase</td>\n",
" <td>mRNA</td>\n",
" <td>157348</td>\n",
" <td>181305</td>\n",
" <td>-1</td>\n",
" <td>-</td>\n",
" <td>-1</td>\n",
" <td>AGAP004677-RA</td>\n",
" <td>.</td>\n",
" <td>AGAP004677</td>\n",
" <td>protein_coding</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>2L</td>\n",
" <td>VectorBase</td>\n",
" <td>three_prime_UTR</td>\n",
" <td>157348</td>\n",
" <td>157495</td>\n",
" <td>-1</td>\n",
" <td>-</td>\n",
" <td>-1</td>\n",
" <td>.</td>\n",
" <td>.</td>\n",
" <td>AGAP004677-RA</td>\n",
" <td>.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>2L</td>\n",
" <td>VectorBase</td>\n",
" <td>exon</td>\n",
" <td>157348</td>\n",
" <td>157623</td>\n",
" <td>-1</td>\n",
" <td>-</td>\n",
" <td>-1</td>\n",
" <td>.</td>\n",
" <td>AGAP004677-RB-E4</td>\n",
" <td>AGAP004677-RA</td>\n",
" <td>.</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" seqid source type start end score strand phase \\\n",
"0 2L VectorBase chromosome 1 49364325 -1 . -1 \n",
"1 2L VectorBase gene 157348 186936 -1 - -1 \n",
"2 2L VectorBase mRNA 157348 181305 -1 - -1 \n",
"3 2L VectorBase three_prime_UTR 157348 157495 -1 - -1 \n",
"4 2L VectorBase exon 157348 157623 -1 - -1 \n",
"\n",
" ID Name Parent biotype \n",
"0 2L . . . \n",
"1 AGAP004677 . . protein_coding \n",
"2 AGAP004677-RA . AGAP004677 protein_coding \n",
"3 . . AGAP004677-RA . \n",
"4 . AGAP004677-RB-E4 AGAP004677-RA . "
]
},
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df_geneset = allel.gff3_to_dataframe('Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.12.gff3.gz',\n",
" attributes=['ID', 'Name', 'Parent', 'biotype'])\n",
"df_geneset.head()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
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"pygments_lexer": "ipython3",
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}
},
"nbformat": 4,
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