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docs: add basic speed test (#17)
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@jsstevenson
jsstevenson authored Jan 18, 2024
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Expand Up @@ -76,3 +76,6 @@ docs/_build/
*.chain

Cargo.lock

# jupyter
.ipynb_checkpoints
364 changes: 364 additions & 0 deletions analysis/speed_test.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"id": "e70c802c-9a54-41e2-a928-7ea685017195",
"metadata": {},
"source": [
"Don't forget to run `maturin develop --release`!"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "856fbc60-6896-4824-8956-b466e29ddc69",
"metadata": {},
"outputs": [],
"source": [
"from pyliftover import LiftOver \n",
"from chainlifter.lifter import ChainLifter"
]
},
{
"cell_type": "markdown",
"id": "63a1308c-e230-43c5-9854-9465eaf2e5d3",
"metadata": {},
"source": [
"# hg38 -> hg19"
]
},
{
"cell_type": "markdown",
"id": "ebf17775-e59d-4b29-b7c1-887c5e7bbbf8",
"metadata": {},
"source": [
"## Load chainfile"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "58db1fb1-2a74-42cc-b586-c169bd396dee",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"1.33 s ± 161 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
]
}
],
"source": [
"%%timeit\n",
"pyl = LiftOver(\"hg38\", \"hg19\")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "2332acf9-c6eb-42ac-8426-fe46eba132a0",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"234 ms ± 7.96 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
]
}
],
"source": [
"%%timeit\n",
"ch = ChainLifter(\"hg38\", \"hg19\")"
]
},
{
"cell_type": "markdown",
"id": "1ef1f123-9d01-4215-90d9-102a117a3ff3",
"metadata": {},
"source": [
"## Load chainfile, run a query"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "ae47dbbb-c9ad-46b4-9f4d-14823bbf26f2",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"1.2 s ± 27.8 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
]
}
],
"source": [
"%%timeit\n",
"pyl = LiftOver(\"hg38\", \"hg19\")\n",
"pyl.convert_coordinate(\"chr5\", 1404391, \"+\")"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "729abc9a-6429-4cb6-aaca-4bac4cd762f8",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"233 ms ± 5.7 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
]
}
],
"source": [
"%%timeit\n",
"ch = ChainLifter(\"hg38\", \"hg19\")\n",
"ch.convert_coordinate(\"chr5\", 1404391, \"+\")"
]
},
{
"cell_type": "markdown",
"id": "f9beb803-8e66-4fb3-9465-6fa941737665",
"metadata": {},
"source": [
"## Run a query"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "7c51c0cb-e997-4ece-8a68-8e946b9dde3d",
"metadata": {},
"outputs": [],
"source": [
"# load beforehand\n",
"pyl = LiftOver(\"hg38\", \"hg19\")\n",
"ch = ChainLifter(\"hg38\", \"hg19\")"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "b68a6af6-1a89-414f-b4f1-2378f3c4f50d",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"2.07 µs ± 67.4 ns per loop (mean ± std. dev. of 7 runs, 100,000 loops each)\n"
]
}
],
"source": [
"%%timeit\n",
"pyl.convert_coordinate(\"chr5\", 1404391, \"+\")"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "e6643c38-f9f5-4ed6-a277-9642e731e6bc",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"1.97 µs ± 12.6 ns per loop (mean ± std. dev. of 7 runs, 1,000,000 loops each)\n"
]
}
],
"source": [
"%%timeit\n",
"ch.convert_coordinate(\"chr5\", 1404391, \"+\")"
]
},
{
"cell_type": "markdown",
"id": "28575012-e1c8-42c0-bea0-1f5cd11926dc",
"metadata": {},
"source": [
"# hg19 -> hg38"
]
},
{
"cell_type": "markdown",
"id": "bbda14b1-11d1-48ae-8687-2c6f6bb21877",
"metadata": {},
"source": [
"## Load chainfile"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "181231d8-3f00-407b-86a3-1ae268d4d931",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"335 ms ± 16.9 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
]
}
],
"source": [
"%%timeit\n",
"pyl = LiftOver(\"hg19\", \"hg38\")"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "7822b8e7-939d-4b6d-85f6-514999c55602",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"63.2 ms ± 773 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
]
}
],
"source": [
"%%timeit\n",
"ch = ChainLifter(\"hg19\", \"hg38\")"
]
},
{
"cell_type": "markdown",
"id": "207fe64e-f84f-4f7f-861e-6eb23574c5c1",
"metadata": {},
"source": [
"## Load chainfile, run a query"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "0ab6aeb8-88da-45e8-9efe-8b4a7825bcff",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"321 ms ± 6.01 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
]
}
],
"source": [
"%%timeit\n",
"pyl = LiftOver(\"hg19\", \"hg38\")\n",
"pyl.convert_coordinate(\"chr5\", 1404391, \"+\")"
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "a014955a-5451-4b10-83bd-4d4843ddc227",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"63.5 ms ± 806 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
]
}
],
"source": [
"%%timeit\n",
"ch = ChainLifter(\"hg19\", \"hg38\")\n",
"ch.convert_coordinate(\"chr5\", 1404391, \"+\")"
]
},
{
"cell_type": "markdown",
"id": "088055d4-0d09-4e12-8826-b3ea39ab94e5",
"metadata": {},
"source": [
"## Run a query"
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "a516e0a8-02b1-4ce5-8e69-3d0badcaffa4",
"metadata": {},
"outputs": [],
"source": [
"# load beforehand\n",
"pyl = LiftOver(\"hg19\", \"hg38\")\n",
"ch = ChainLifter(\"hg19\", \"hg38\")"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "d433fee3-9c40-4633-be5e-2649b723968e",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"2.02 µs ± 11.6 ns per loop (mean ± std. dev. of 7 runs, 100,000 loops each)\n"
]
}
],
"source": [
"%%timeit\n",
"pyl.convert_coordinate(\"chr5\", 1404391, \"+\")"
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "5bb82164-e123-47ae-a748-7d4c4898fcb2",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"2.02 µs ± 56 ns per loop (mean ± std. dev. of 7 runs, 100,000 loops each)\n"
]
}
],
"source": [
"%%timeit\n",
"ch.convert_coordinate(\"chr5\", 1404391, \"+\")"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "liftovertest",
"language": "python",
"name": "liftovertest"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.0"
}
},
"nbformat": 4,
"nbformat_minor": 5
}

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