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VictorGarritano/coffee.ipynb

Created September 11, 2017 01:19
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coffee.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import metabolomic as meta\n",
"import timeit\n",
"\n",
"df = meta.load_database('DB_Coffee_V00.xlsx', parse_cols='A:L, N:P')"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"base_de_dados = df\n",
"arquivo_de_massas = 'Dados_Positivo.csv'\n",
"modo = 'pos'\n",
"exportar_resultados = False\n",
"fi2 = meta.search_by_mass(df=base_de_dados,\n",
" mass_file=arquivo_de_massas,\n",
" mode=modo,\n",
" export=exportar_resultados)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(15, 6)"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"fi2.shape"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style>\n",
" .dataframe thead tr:only-child th {\n",
" text-align: right;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: left;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Compounds</th>\n",
" <th>Chemical Formula</th>\n",
" <th>MW</th>\n",
" <th>match</th>\n",
" <th>reference_value</th>\n",
" <th>ppm_value</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>arabinose</td>\n",
" <td>C5H10O5</td>\n",
" <td>150.053</td>\n",
" <td>[M+H-H2O]+</td>\n",
" <td>133.05</td>\n",
" <td>0.15032</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>xylose</td>\n",
" <td>C5H10O5</td>\n",
" <td>150.053</td>\n",
" <td>[M+H-H2O]+</td>\n",
" <td>133.05</td>\n",
" <td>0.15032</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>trigonelline</td>\n",
" <td>C7H7NO2+</td>\n",
" <td>137.048</td>\n",
" <td>[M+H]+</td>\n",
" <td>138.055</td>\n",
" <td>-0.724349</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>caffeic acid</td>\n",
" <td>C9H8O4</td>\n",
" <td>180.042</td>\n",
" <td>[M+H-H2O]+</td>\n",
" <td>163.039</td>\n",
" <td>-0.797355</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>agmatine</td>\n",
" <td>C5H14N4</td>\n",
" <td>130.122</td>\n",
" <td>[M+K]+</td>\n",
" <td>169.086</td>\n",
" <td>4.98921</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>caffeic acid</td>\n",
" <td>C9H8O4</td>\n",
" <td>180.042</td>\n",
" <td>[M+H]+</td>\n",
" <td>181.049</td>\n",
" <td>-0.552335</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>syringic acid</td>\n",
" <td>C9H10O5</td>\n",
" <td>198.053</td>\n",
" <td>[M+H-H2O]+</td>\n",
" <td>181.049</td>\n",
" <td>-0.552335</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>Caffeine</td>\n",
" <td>C8H10N4O2</td>\n",
" <td>194.08</td>\n",
" <td>[M+H]+</td>\n",
" <td>195.088</td>\n",
" <td>-0.666367</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>4-(furan-2-ylmethyl)-5-methylbenzene-1,2-diol</td>\n",
" <td>C12H12O3</td>\n",
" <td>204.079</td>\n",
" <td>[M+H]+</td>\n",
" <td>205.086</td>\n",
" <td>-0.14628</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>4-(furan-2-ylmethyl)-5-methylbenzene-1,2-diol</td>\n",
" <td>C12H12O3</td>\n",
" <td>204.079</td>\n",
" <td>[M+NH4]+</td>\n",
" <td>222.112</td>\n",
" <td>-0.495245</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>myristic acid (C14:0)</td>\n",
" <td>C14H28O2</td>\n",
" <td>228.209</td>\n",
" <td>[M+COOH]+</td>\n",
" <td>273.206</td>\n",
" <td>-1.13467</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>caffeoylquinic acid isomers</td>\n",
" <td>C16H18O9</td>\n",
" <td>354.095</td>\n",
" <td>[M+H]+</td>\n",
" <td>355.102</td>\n",
" <td>-1.01379</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>sucrose</td>\n",
" <td>C12H22O11</td>\n",
" <td>342.116</td>\n",
" <td>[M+NH4]+</td>\n",
" <td>360.15</td>\n",
" <td>-1.41608</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>feruloylquinic acid isomers</td>\n",
" <td>C17H20O9</td>\n",
" <td>368.111</td>\n",
" <td>[M+H]+</td>\n",
" <td>369.118</td>\n",
" <td>-1.08366</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>sucrose</td>\n",
" <td>C12H22O11</td>\n",
" <td>342.116</td>\n",
" <td>[M+K]+</td>\n",
" <td>381.079</td>\n",
" <td>-1.67944</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" Compounds Chemical Formula MW \\\n",
"0 arabinose C5H10O5 150.053 \n",
"1 xylose C5H10O5 150.053 \n",
"0 trigonelline C7H7NO2+ 137.048 \n",
"0 caffeic acid C9H8O4 180.042 \n",
"0 agmatine C5H14N4 130.122 \n",
"0 caffeic acid C9H8O4 180.042 \n",
"1 syringic acid C9H10O5 198.053 \n",
"0 Caffeine C8H10N4O2 194.08 \n",
"0 4-(furan-2-ylmethyl)-5-methylbenzene-1,2-diol C12H12O3 204.079 \n",
"0 4-(furan-2-ylmethyl)-5-methylbenzene-1,2-diol C12H12O3 204.079 \n",
"0 myristic acid (C14:0) C14H28O2 228.209 \n",
"0 caffeoylquinic acid isomers C16H18O9 354.095 \n",
"0 sucrose C12H22O11 342.116 \n",
"0 feruloylquinic acid isomers C17H20O9 368.111 \n",
"0 sucrose C12H22O11 342.116 \n",
"\n",
" match reference_value ppm_value \n",
"0 [M+H-H2O]+ 133.05 0.15032 \n",
"1 [M+H-H2O]+ 133.05 0.15032 \n",
"0 [M+H]+ 138.055 -0.724349 \n",
"0 [M+H-H2O]+ 163.039 -0.797355 \n",
"0 [M+K]+ 169.086 4.98921 \n",
"0 [M+H]+ 181.049 -0.552335 \n",
"1 [M+H-H2O]+ 181.049 -0.552335 \n",
"0 [M+H]+ 195.088 -0.666367 \n",
"0 [M+H]+ 205.086 -0.14628 \n",
"0 [M+NH4]+ 222.112 -0.495245 \n",
"0 [M+COOH]+ 273.206 -1.13467 \n",
"0 [M+H]+ 355.102 -1.01379 \n",
"0 [M+NH4]+ 360.15 -1.41608 \n",
"0 [M+H]+ 369.118 -1.08366 \n",
"0 [M+K]+ 381.079 -1.67944 "
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"fi2"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
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},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
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"nbformat_minor": 2
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