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@gregcaporaso
Created November 6, 2014 22:59
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comparison of runtime for single_rarefaction.py in QIIME 1.8.0 and 1.8.0-dev
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{
"metadata": {
"name": "",
"signature": "sha256:08ad309f1d4e7e35e9665af74d65e02e2bbf77ca41636083884f999a4e766136"
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"worksheets": [
{
"cells": [
{
"cell_type": "code",
"collapsed": false,
"input": [
"from __future__ import division\n",
"from timeit import timeit\n",
"from biom import load_table\n",
"import pandas as pd\n",
"from glob import glob\n",
"\n",
"t = load_table('table_mc5038.biom')"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 19
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"t.shape"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 2,
"text": [
"(52663, 396)"
]
}
],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"axes = ['observation', 'sample']\n",
"shape = t.shape\n",
"\n",
"for i, axis in enumerate(axes):\n",
" data[axis] = []\n",
" step_size = np.ceil(shape[i] / 10)\n",
" for n in arange(step_size, shape[i], step_size):\n",
" ids = t.ids(axis=axis)[:n]\n",
" subt = t.filter(ids, axis=axis, inplace=False)\n",
" out_path = 'test-tables/t.%d.%s.biom' % (n, axis)\n",
" subt.to_json('me', open(out_path, 'w'))"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 16
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"data = {'observation': [], 'sample': []}\n",
"for fp in glob('test-tables/t.*.biom'):\n",
" fields = fp.split('.')\n",
" n = fields[1]\n",
" axis = fields[2]\n",
" def sr():\n",
" !single_rarefaction.py -i $fp -o x.biom -d 500\n",
" data[axis].append((int(n), timeit(sr, number=3) / 3))"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 21
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"df = pd.DataFrame(data['observation'], columns=['n', 'mean run time'], dtype=float)\n",
"df.sort('n', inplace=True)\n",
"df.plot(x='n', y='mean run time')"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 39,
"text": [
"<matplotlib.axes.AxesSubplot at 0x117c26290>"
]
},
{
"metadata": {},
"output_type": "display_data",
"png": 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hvPoqNGkCr70Gf/sbfP453HBD7Ip1vI6dLdTDFklwu3fDP/5hCnTr1qZP3b6926nEZuph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\nzv95XAAAAABJRU5ErkJggg==\n",
"text": [
"<matplotlib.figure.Figure at 0x118573890>"
]
}
],
"prompt_number": 39
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"df = pd.DataFrame(data['sample'], columns=['n', 'mean run time'], dtype=float)\n",
"df.sort('n', inplace=True)\n",
"df.plot(x='n', y='mean run time', legend=False)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 38,
"text": [
"<matplotlib.axes.AxesSubplot at 0x10de7e5d0>"
]
},
{
"metadata": {},
"output_type": "display_data",
"png": 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"text": [
"<matplotlib.figure.Figure at 0x114673a50>"
]
}
],
"prompt_number": 38
},
{
"cell_type": "code",
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