nbs/test_alphatims_wrapper.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "%reload_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:root:WARNING: Temp mmap arrays are written to /var/folders/hn/0f5pbk7j55sd4r5bxjp25_rm0000gn/T/temp_mmap_8rdci3ad. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 841062969344\n",
      "WARNING:root:WARNING: No Bruker libraries are available for this operating system. Mobility and m/z values need to be estimated. While this estimation often returns acceptable results with errors < 0.02 Th, huge errors (e.g. offsets of 6 Th) have already been observed for some samples!\n"
     ]
    }
   ],
   "source": [
    "from alpharaw.thermo import ThermoRawData\n",
    "from alpharaw.wrappers.alphatims_wrapper import AlphaTimsWrapper"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
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       "      spec_idx  peak_start_idx  peak_stop_idx        rt  ms_level  \\\n",
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       "\n",
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      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "raw_data = ThermoRawData()\n",
    "raw_data.import_raw(\"/Users/zengwenfeng/Workspace/Data/Thermo_iRT/iRT.raw\")\n",
    "raw_data.spectrum_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
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     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "raw_data.peak_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>11751726</td>\n",
       "      <td>0.998447</td>\n",
       "      <td>0.016641</td>\n",
       "      <td>0</td>\n",
       "      <td>-1.0</td>\n",
       "      <td>-1.0</td>\n",
       "      <td>1275.1726</td>\n",
       "      <td>4921.953613</td>\n",
       "      <td>4921</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2168</th>\n",
       "      <td>2168</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>12630518</td>\n",
       "      <td>0.998447</td>\n",
       "      <td>0.016641</td>\n",
       "      <td>0</td>\n",
       "      <td>-1.0</td>\n",
       "      <td>-1.0</td>\n",
       "      <td>1363.0518</td>\n",
       "      <td>5242.800781</td>\n",
       "      <td>5242</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2169 rows × 14 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      raw_indices  frame_indices  scan_indices  precursor_indices  \\\n",
       "0               0              0             0                  0   \n",
       "1               1              0             0                  0   \n",
       "2               2              0             0                  0   \n",
       "3               3              0             0                  0   \n",
       "4               4              0             0                  0   \n",
       "...           ...            ...           ...                ...   \n",
       "2164         2164              4             0                  0   \n",
       "2165         2165              4             0                  0   \n",
       "2166         2166              4             0                  0   \n",
       "2167         2167              4             0                  0   \n",
       "2168         2168              4             0                  0   \n",
       "\n",
       "      push_indices  tof_indices  rt_values  rt_values_min  mobility_values  \\\n",
       "0                0      2010603   0.178981       0.002983                0   \n",
       "1                0      2011429   0.178981       0.002983                0   \n",
       "2                0      2012173   0.178981       0.002983                0   \n",
       "3                0      2012389   0.178981       0.002983                0   \n",
       "4                0      2019768   0.178981       0.002983                0   \n",
       "...            ...          ...        ...            ...              ...   \n",
       "2164             4      9978870   0.998447       0.016641                0   \n",
       "2165             4     10016389   0.998447       0.016641                0   \n",
       "2166             4     10263106   0.998447       0.016641                0   \n",
       "2167             4     11751726   0.998447       0.016641                0   \n",
       "2168             4     12630518   0.998447       0.016641                0   \n",
       "\n",
       "      quad_low_mz_values  quad_high_mz_values  mz_values  intensity_values  \\\n",
       "0                   -1.0                 -1.0   301.0603      36817.058594   \n",
       "1                   -1.0                 -1.0   301.1429      12673.902344   \n",
       "2                   -1.0                 -1.0   301.2173      53082.824219   \n",
       "3                   -1.0                 -1.0   301.2389      16699.697266   \n",
       "4                   -1.0                 -1.0   301.9768      27308.283203   \n",
       "...                  ...                  ...        ...               ...   \n",
       "2164                -1.0                 -1.0  1097.8870       5626.406738   \n",
       "2165                -1.0                 -1.0  1101.6389       5588.583984   \n",
       "2166                -1.0                 -1.0  1126.3106       4457.186035   \n",
       "2167                -1.0                 -1.0  1275.1726       4921.953613   \n",
       "2168                -1.0                 -1.0  1363.0518       5242.800781   \n",
       "\n",
       "      corrected_intensity_values  \n",
       "0                          36817  \n",
       "1                          12673  \n",
       "2                          53082  \n",
       "3                          16699  \n",
       "4                          27308  \n",
       "...                          ...  \n",
       "2164                        5626  \n",
       "2165                        5588  \n",
       "2166                        4457  \n",
       "2167                        4921  \n",
       "2168                        5242  \n",
       "\n",
       "[2169 rows x 14 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "alphatims_data = AlphaTimsWrapper(raw_data, dda=True)\n",
    "alphatims_data[0.0:1.0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <td>5281</td>\n",
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       "      <td>4659</td>\n",
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       "  </tbody>\n",
       "</table>\n",
       "<p>5235 rows × 14 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        raw_indices  frame_indices  scan_indices  precursor_indices  \\\n",
       "155270       155270            297             0                  1   \n",
       "155271       155271            297             0                  1   \n",
       "155272       155272            297             0                  1   \n",
       "155273       155273            297             0                  1   \n",
       "155274       155274            297             0                  1   \n",
       "...             ...            ...           ...                ...   \n",
       "236460       236460            619             0                153   \n",
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       "236463       236463            619             0                153   \n",
       "236464       236464            619             0                153   \n",
       "\n",
       "        push_indices  tof_indices  rt_values  rt_values_min  mobility_values  \\\n",
       "155270           297       749929   60.75817       1.012636                0   \n",
       "155271           297       890955   60.75817       1.012636                0   \n",
       "155272           297       988056   60.75817       1.012636                0   \n",
       "155273           297      1284147   60.75817       1.012636                0   \n",
       "155274           297      1510011   60.75817       1.012636                0   \n",
       "...              ...          ...        ...            ...              ...   \n",
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       "236461           619      1621494   99.48445       1.658074                0   \n",
       "236462           619      2221251   99.48445       1.658074                0   \n",
       "236463           619      2341224   99.48445       1.658074                0   \n",
       "236464           619      2557881   99.48445       1.658074                0   \n",
       "\n",
       "        quad_low_mz_values  quad_high_mz_values  mz_values  intensity_values  \\\n",
       "155270          326.309033           327.709033   174.9929      38397.171875   \n",
       "155271          326.309033           327.709033   189.0955       4517.982910   \n",
       "155272          326.309033           327.709033   198.8056       4471.824219   \n",
       "155273          326.309033           327.709033   228.4147       5381.021484   \n",
       "155274          326.309033           327.709033   251.0011       6580.025391   \n",
       "...                    ...                  ...        ...               ...   \n",
       "236460          408.506360           409.906360   208.1704       4012.170410   \n",
       "236461          408.506360           409.906360   262.1494       5135.653320   \n",
       "236462          408.506360           409.906360   322.1251      18180.195312   \n",
       "236463          408.506360           409.906360   334.1224       5281.465332   \n",
       "236464          408.506360           409.906360   355.7881       4659.617676   \n",
       "\n",
       "        corrected_intensity_values  \n",
       "155270                       38397  \n",
       "155271                        4517  \n",
       "155272                        4471  \n",
       "155273                        5381  \n",
       "155274                        6580  \n",
       "...                            ...  \n",
       "236460                        4012  \n",
       "236461                        5135  \n",
       "236462                       18180  \n",
       "236463                        5281  \n",
       "236464                        4659  \n",
       "\n",
       "[5235 rows x 14 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "alphatims_data[0.0:100.0].query('precursor_indices>0')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Test iRT DIA data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <td>478.5</td>\n",
       "      <td>0</td>\n",
       "      <td>467.5</td>\n",
       "      <td>489.5</td>\n",
       "      <td>359.829409</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4377</th>\n",
       "      <td>4377</td>\n",
       "      <td>1225601</td>\n",
       "      <td>1225796</td>\n",
       "      <td>5.998308</td>\n",
       "      <td>2</td>\n",
       "      <td>498.0</td>\n",
       "      <td>0</td>\n",
       "      <td>488.5</td>\n",
       "      <td>507.5</td>\n",
       "      <td>359.898502</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4378</th>\n",
       "      <td>4378</td>\n",
       "      <td>1225796</td>\n",
       "      <td>1225996</td>\n",
       "      <td>5.999455</td>\n",
       "      <td>2</td>\n",
       "      <td>516.5</td>\n",
       "      <td>0</td>\n",
       "      <td>506.5</td>\n",
       "      <td>526.5</td>\n",
       "      <td>359.967279</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4379</th>\n",
       "      <td>4379</td>\n",
       "      <td>1225996</td>\n",
       "      <td>1226145</td>\n",
       "      <td>6.000605</td>\n",
       "      <td>2</td>\n",
       "      <td>534.5</td>\n",
       "      <td>0</td>\n",
       "      <td>525.5</td>\n",
       "      <td>543.5</td>\n",
       "      <td>360.036319</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4380</th>\n",
       "      <td>4380</td>\n",
       "      <td>1226145</td>\n",
       "      <td>1226313</td>\n",
       "      <td>6.001752</td>\n",
       "      <td>2</td>\n",
       "      <td>552.0</td>\n",
       "      <td>0</td>\n",
       "      <td>542.5</td>\n",
       "      <td>561.5</td>\n",
       "      <td>360.105099</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4381 rows × 10 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      spec_idx  peak_start_idx  peak_stop_idx        rt  ms_level  \\\n",
       "0            0               0           255  0.002871         1   \n",
       "1            1             255           444  0.008945         2   \n",
       "2            2             444           531  0.010096         2   \n",
       "3            3             531           613  0.011247         2   \n",
       "4            4             613           677  0.012398         2   \n",
       "...        ...             ...           ...       ...       ...   \n",
       "4376      4376         1225345       1225601  5.997157         2   \n",
       "4377      4377         1225601       1225796  5.998308         2   \n",
       "4378      4378         1225796       1225996  5.999455         2   \n",
       "4379      4379         1225996       1226145  6.000605         2   \n",
       "4380      4380         1226145       1226313  6.001752         2   \n",
       "\n",
       "      precursor_mz  charge  isolation_lower_mz  isolation_upper_mz      rt_sec  \n",
       "0             -1.0       0                -1.0                -1.0    0.172236  \n",
       "1            371.0       0               349.5               392.5    0.536688  \n",
       "2            407.0       0               391.5               422.5    0.605779  \n",
       "3            434.5       0               421.5               447.5    0.674839  \n",
       "4            457.5       0               446.5               468.5    0.743904  \n",
       "...            ...     ...                 ...                 ...         ...  \n",
       "4376         478.5       0               467.5               489.5  359.829409  \n",
       "4377         498.0       0               488.5               507.5  359.898502  \n",
       "4378         516.5       0               506.5               526.5  359.967279  \n",
       "4379         534.5       0               525.5               543.5  360.036319  \n",
       "4380         552.0       0               542.5               561.5  360.105099  \n",
       "\n",
       "[4381 rows x 10 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "raw_data = ThermoRawData()\n",
    "raw_data.import_raw(\"/Users/zengwenfeng/Workspace/Data/Thermo_iRT/DIA/20200911_EXPL0_IgPa_6min_DIA_2.raw\")\n",
    "raw_data.spectrum_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
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       "</table>\n",
       "<p>6056 rows × 14 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      raw_indices  frame_indices  scan_indices  precursor_indices  \\\n",
       "0               0              0             0                  0   \n",
       "1               1              0             0                  0   \n",
       "2               2              0             0                  0   \n",
       "3               3              0             0                  0   \n",
       "4               4              0             0                  0   \n",
       "...           ...            ...           ...                ...   \n",
       "6051         6051            118             0                 25   \n",
       "6052         6052            118             0                 25   \n",
       "6053         6053            118             0                 25   \n",
       "6054         6054            118             0                 25   \n",
       "6055         6055            118             0                 25   \n",
       "\n",
       "      push_indices  tof_indices  rt_values  rt_values_min  mobility_values  \\\n",
       "0                0      2311488   0.172236       0.002871                0   \n",
       "1                0      2320976   0.172236       0.002871                0   \n",
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       "...            ...          ...        ...            ...              ...   \n",
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       "6054           118      7425253   9.991487       0.166525                0   \n",
       "6055           118     26372370   9.991487       0.166525                0   \n",
       "\n",
       "      quad_low_mz_values  quad_high_mz_values  mz_values  intensity_values  \\\n",
       "0                   -1.0                 -1.0   351.1488      15592.084961   \n",
       "1                   -1.0                 -1.0   352.0976       6126.446777   \n",
       "2                   -1.0                 -1.0   352.8230       4330.460449   \n",
       "3                   -1.0                 -1.0   352.8887       4539.788574   \n",
       "4                   -1.0                 -1.0   353.9421       4448.501953   \n",
       "...                  ...                  ...        ...               ...   \n",
       "6051               907.5                959.5   555.6066       1283.586792   \n",
       "6052               907.5                959.5   561.1621       1296.302979   \n",
       "6053               907.5                959.5   744.7720       1474.562500   \n",
       "6054               907.5                959.5   862.5253       1413.956787   \n",
       "6055               907.5                959.5  2757.2370       1703.588623   \n",
       "\n",
       "      corrected_intensity_values  \n",
       "0                          15592  \n",
       "1                           6126  \n",
       "2                           4330  \n",
       "3                           4539  \n",
       "4                           4448  \n",
       "...                          ...  \n",
       "6051                        1283  \n",
       "6052                        1296  \n",
       "6053                        1474  \n",
       "6054                        1413  \n",
       "6055                        1703  \n",
       "\n",
       "[6056 rows x 14 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "alphatims_data = AlphaTimsWrapper(raw_data, dda=False)\n",
    "alphatims_data[0.0:10.0]"
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  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "     precursor_indices  push_indices\n",
       "0                    0             0\n",
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    "alphatims_data[0.0:1.0][['precursor_indices','push_indices']].drop_duplicates()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      precursor_indices  push_indices\n",
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   "source": [
    "alphatims_data[0.0:10.0].query('precursor_indices==0')[\n",
    "    ['precursor_indices','push_indices']\n",
    "].drop_duplicates()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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