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Julianus Pfeuffer
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Added nb for featureXML
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‎PyopenmsPandas.ipynb

+451-1
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‎featureXML.ipynb

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{
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"cells": [
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{
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"metadata": {
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"trusted": true
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},
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"cell_type": "code",
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"source": [
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"from collections import defaultdict\n",
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"from functools import reduce\n",
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"from pathlib import Path\n",
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"from time import perf_counter\n",
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"import sys\n",
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"\n",
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"from IPython.core.display import display\n",
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"from pandas import CategoricalDtype\n",
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"import numpy as np\n",
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"from pyopenms import *\n",
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"import pandas as pd\n",
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"import os"
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],
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"execution_count": 24,
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"outputs": []
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},
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{
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"metadata": {
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"trusted": true
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},
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"cell_type": "code",
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"source": [
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"class FeatureMapDF(FeatureMap):\n",
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" def __init__(self):\n",
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" super().__init__()\n",
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"\n",
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" def get_df(self):\n",
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" def gen(fmap: FeatureMap, fun):\n",
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" for f in fmap:\n",
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" yield from fun(f)\n",
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"\n",
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" def extractMetaData(f: Feature):\n",
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" # subfeatures = f.getFeatureList() # type: list[FeatureHandle]\n",
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" pep = f.getPeptideIdentifications() # type: list[PeptideIdentification]\n",
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" if len(pep) != 0:\n",
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" hits = pep[0].getHits()\n",
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" if len(hits) != 0:\n",
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" besthit = hits[0] # type: PeptideHit\n",
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" # TODO what else\n",
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" yield f.getUniqueId(), besthit.getSequence().toString(), f.getCharge(), f.getRT(), f.getMZ(), f.getOverallQuality(), f.getIntensity()\n",
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" else:\n",
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" yield f.getUniqueId(), None, f.getCharge(), f.getRT(), f.getMZ(), f.getOverallQuality(), f.getIntensity()\n",
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" else:\n",
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" yield f.getUniqueId(), None, f.getCharge(), f.getRT(), f.getMZ(), f.getOverallQuality(), f.getIntensity()\n",
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"\n",
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" cnt = self.size()\n",
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"\n",
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" mddtypes = [('id', np.dtype('uint64')), ('sequence', 'U200'), ('charge', 'i4'), ('RT', 'f'), ('mz', 'f'),\n",
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" ('quality', 'f'), ('intensity', 'f')]\n",
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" mdarr = np.fromiter(iter=gen(self, extractMetaData), dtype=mddtypes, count=cnt)\n",
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" return pd.DataFrame(mdarr).set_index('id')"
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],
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"execution_count": 25,
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"outputs": []
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},
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{
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"metadata": {
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"trusted": true
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},
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"cell_type": "code",
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"source": [
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"fmap = FeatureMapDF()\n",
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"from urllib.request import urlretrieve\n",
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"urlretrieve (\"https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/examples/FRACTIONS/BSA1_F1.featureXML\", \"BSA1.featureXML\")\n",
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"\n",
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"FeatureXMLFile().load(\"BSA1.featureXML\", fmap)\n",
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" "
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],
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"execution_count": 26,
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"outputs": []
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},
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{
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"metadata": {
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"trusted": true,
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"pycharm": {
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"name": "#%%\n"
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}
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},
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"cell_type": "code",
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"source": [
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"display(fmap.get_df())"
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],
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"execution_count": 27,
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"outputs": [
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{
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"data": {
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"text/plain": " sequence charge RT mz quality \\\nid \n9650885788371886430 None 2 1942.600098 395.239288 0.808494 \n18416216708636999474 None 2 1749.138306 443.711212 0.893553 \n4391849314104099247 None 3 1850.058960 325.491180 0.788273 \n8826587690601962141 None 1 1977.238281 388.253906 0.844645 \n446423704489322421 None 2 1901.577637 738.311035 0.770521 \n... ... ... ... ... ... \n10302832019150983352 None 3 1606.777588 426.142517 0.838608 \n8874676592351452214 None 3 1531.052490 403.509857 0.806600 \n2099235613780550198 None 1 1679.266113 344.091949 0.750061 \n16983971133852021113 None 1 1542.787109 330.191254 0.742557 \n11071931317879296440 None 2 1658.548828 485.347015 0.842046 \n\n intensity \nid \n9650885788371886430 1.575720e+08 \n18416216708636999474 5.406930e+07 \n4391849314104099247 5.271700e+07 \n8826587690601962141 3.802820e+07 \n446423704489322421 3.498880e+07 \n... ... \n10302832019150983352 3.678150e+04 \n8874676592351452214 3.128000e+04 \n2099235613780550198 3.097710e+04 \n16983971133852021113 2.789520e+04 \n11071931317879296440 2.438280e+04 \n\n[256 rows x 6 columns]",
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"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>sequence</th>\n <th>charge</th>\n <th>RT</th>\n <th>mz</th>\n <th>quality</th>\n <th>intensity</th>\n </tr>\n <tr>\n <th>id</th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n <th></th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th>9650885788371886430</th>\n <td>None</td>\n <td>2</td>\n <td>1942.600098</td>\n <td>395.239288</td>\n <td>0.808494</td>\n <td>1.575720e+08</td>\n </tr>\n <tr>\n <th>18416216708636999474</th>\n <td>None</td>\n <td>2</td>\n <td>1749.138306</td>\n <td>443.711212</td>\n <td>0.893553</td>\n <td>5.406930e+07</td>\n </tr>\n <tr>\n <th>4391849314104099247</th>\n <td>None</td>\n <td>3</td>\n <td>1850.058960</td>\n <td>325.491180</td>\n <td>0.788273</td>\n <td>5.271700e+07</td>\n </tr>\n <tr>\n <th>8826587690601962141</th>\n <td>None</td>\n <td>1</td>\n <td>1977.238281</td>\n <td>388.253906</td>\n <td>0.844645</td>\n <td>3.802820e+07</td>\n </tr>\n <tr>\n <th>446423704489322421</th>\n <td>None</td>\n <td>2</td>\n <td>1901.577637</td>\n <td>738.311035</td>\n <td>0.770521</td>\n <td>3.498880e+07</td>\n </tr>\n <tr>\n <th>...</th>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n <td>...</td>\n </tr>\n <tr>\n <th>10302832019150983352</th>\n <td>None</td>\n <td>3</td>\n <td>1606.777588</td>\n <td>426.142517</td>\n <td>0.838608</td>\n <td>3.678150e+04</td>\n </tr>\n <tr>\n <th>8874676592351452214</th>\n <td>None</td>\n <td>3</td>\n <td>1531.052490</td>\n <td>403.509857</td>\n <td>0.806600</td>\n <td>3.128000e+04</td>\n </tr>\n <tr>\n <th>2099235613780550198</th>\n <td>None</td>\n <td>1</td>\n <td>1679.266113</td>\n <td>344.091949</td>\n <td>0.750061</td>\n <td>3.097710e+04</td>\n </tr>\n <tr>\n <th>16983971133852021113</th>\n <td>None</td>\n <td>1</td>\n <td>1542.787109</td>\n <td>330.191254</td>\n <td>0.742557</td>\n <td>2.789520e+04</td>\n </tr>\n <tr>\n <th>11071931317879296440</th>\n <td>None</td>\n <td>2</td>\n <td>1658.548828</td>\n <td>485.347015</td>\n <td>0.842046</td>\n <td>2.438280e+04</td>\n </tr>\n </tbody>\n</table>\n<p>256 rows × 6 columns</p>\n</div>"
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},
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"metadata": {},
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"output_type": "display_data"
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}
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"name": "python3",
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"display_name": "Python 3",
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"language": "python"
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"name": "python",
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"version": "3.7.10",
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"pygments_lexer": "ipython3",
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"nbconvert_exporter": "python",
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"file_extension": ".py"
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},
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"nbformat": 4,
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"nbformat_minor": 1
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}

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