{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "de60eea1",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:rdkit:Enabling RDKit 2021.09.4 jupyter extensions\n"
     ]
    }
   ],
   "source": [
    "import glob\n",
    "import json\n",
    "import os\n",
    "import re\n",
    "import time\n",
    "import wget\n",
    "import urllib.parse\n",
    "import argparse\n",
    "\n",
    "\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import pubchempy as pcp\n",
    "\n",
    "\n",
    "from pybatchclassyfire import *\n",
    "from pandas import json_normalize\n",
    "from rdkit import Chem\n",
    "from rdkit import DataStructs\n",
    "from rdkit.Chem import AllChem\n",
    "from rdkit.Chem import rdFMCS\n",
    "from rdkit.Chem import PandasTools\n",
    "def isNaN(string):\n",
    "    return string != string"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "04f55ddf",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['DS_201124_SC_full_PRM_pos_03',\n",
       " 'DS_201124_SC_full_PRM_pos_04',\n",
       " 'DS200309_Scost_QC_70k_neg_PRM',\n",
       " 'DS_201124_SC_full_PRM_pos_05',\n",
       " 'DS_201124_SC_full_PRM_pos_02',\n",
       " 'DS_201124_SC_full_PRM_neg_03',\n",
       " 'DS_201124_SC_full_PRM_neg_04',\n",
       " 'DS200309_Scost_QC_70k_pos_PRM',\n",
       " 'DS_201124_SC_full_PRM_neg_05',\n",
       " 'DS_201124_SC_full_PRM_neg_02',\n",
       " 'DS_201124_SC_full_PRM_neg_10',\n",
       " 'DS_201124_SC_full_PRM_pos_10',\n",
       " 'DS_201124_SC_full_PRM_pos_07',\n",
       " 'DS_201124_SC_full_PRM_pos_09',\n",
       " 'DS_201124_SC_full_PRM_pos_08',\n",
       " 'DS_201124_SC_full_PRM_pos_01',\n",
       " 'DS_201124_SC_full_PRM_pos_06',\n",
       " 'DS_201124_SC_full_PRM_neg_07',\n",
       " 'DS_201124_SC_full_PRM_neg_09',\n",
       " 'DS_201124_SC_full_PRM_neg_08',\n",
       " 'DS_201124_SC_full_PRM_neg_01',\n",
       " 'DS_201124_SC_full_PRM_neg_06']"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "path = \"/Users/mahnoorzulfiqar/OneDriveUNI/MAW-Diatom/SmarinoiRun1\"\n",
    "file = os.listdir(path)\n",
    "folders = [x for x in os.listdir(path) if x.startswith('DS')]\n",
    "folders2 = [x for x in folders if not '.mzML' in x]\n",
    "folders2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "5c39fb85",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/Users/mahnoorzulfiqar/OneDriveUNI/MAW-Diatom/SmarinoiRun1/DS_201124_SC_full_PRM_pos_03\n"
     ]
    },
    {
     "ename": "NameError",
     "evalue": "name 'sirius_postproc' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "Input \u001b[0;32mIn [3]\u001b[0m, in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      7\u001b[0m \u001b[38;5;28mprint\u001b[39m(entry)\n\u001b[1;32m      8\u001b[0m sirius_dirs \u001b[38;5;241m=\u001b[39m foldersir\n\u001b[0;32m----> 9\u001b[0m \u001b[43msirius_postproc\u001b[49m(entry, sirius_dirs, db \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mSL\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
      "\u001b[0;31mNameError\u001b[0m: name 'sirius_postproc' is not defined"
     ]
    }
   ],
   "source": [
    "for i in folders2:\n",
    "    entry = path + \"/\" + i\n",
    "    sub_dir = entry + \"/insilico/SIRIUS/\"\n",
    "    file = os.listdir(sub_dir)\n",
    "    foldersir = [x for x in os.listdir(sub_dir) if x.endswith('.json')]\n",
    "    foldersir = [x for x in foldersir if 'SList.json' in x]\n",
    "    print(entry)\n",
    "    sirius_dirs = foldersir\n",
    "    sirius_postproc(entry, sirius_dirs, db = \"SL\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 167,
   "id": "359479ed",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/Users/mahnoorzulfiqar/OneDriveUNI/MAW-Diatom/SmarinoiRun1/DS_201124_SC_full_PRM_pos_09'"
      ]
     },
     "execution_count": 167,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "entry"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 172,
   "id": "632e9758",
   "metadata": {},
   "outputs": [],
   "source": [
    "if os.path.isdir(entry + \"/insilico/SIRIUS/\"):\n",
    "    sub_dir = entry + \"/insilico/SIRIUS/\"\n",
    "    msp_csv = entry + \"/insilico/MS1DATA.csv\"\n",
    "    if os.path.exists(msp_csv) and os.path.exists(sub_dir):\n",
    "        # output json files from SIRIUS\n",
    "        files_S = sirius_dirs\n",
    "        # list of precursor m/z\n",
    "        msp = pd.read_csv(msp_csv)\n",
    "        # for each mz\n",
    "        for mz, row in msp.iterrows():\n",
    "            # make a list of files with this mz\n",
    "            files_for_mz = []\n",
    "\n",
    "            for file in files_S:\n",
    "                if str(msp[\"premz\"][mz]) in file:\n",
    "                    files_for_mz.append(file)\n",
    "\n",
    "#             # extract the formula and structure files\n",
    "#             json_dirALL = next(os.walk(sub_dir + files_for_mz[0]))[1]\n",
    "            "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 173,
   "id": "4ca4f25b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[]"
      ]
     },
     "execution_count": 173,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "files_for_mz"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9da3558c",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "31367680",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "896449e3",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "06547c9b",
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "        \n",
    "            if len(json_dirALL) == 1:\n",
    "                sub_sub_dirALL_structure_can = (sub_dir +\n",
    "                    files_for_mz[0]\n",
    "                    + \"/\"\n",
    "                    + json_dirALL[0]\n",
    "                    + \"/structure_candidates.tsv\"\n",
    "                )\n",
    "                sub_sub_dirALL_formula_can = (sub_dir +\n",
    "                    files_for_mz[0]\n",
    "                    + \"/\"\n",
    "                    + json_dirALL[0]\n",
    "                    + \"/formula_candidates.tsv\"\n",
    "                )\n",
    "                ALL_Canopus_csv = sub_dir + files_for_mz[0] + \"/canopus_summary.tsv\"\n",
    "\n",
    "                # if both structure files exist\n",
    "                if (\n",
    "                    os.path.exists(sub_sub_dirALL_structure_can)\n",
    "                    and len(pd.read_csv(sub_sub_dirALL_structure_can, sep=\"\\t\")) > 0\n",
    "                ):\n",
    "                    if (\n",
    "                         os.path.exists(sub_sub_dirALL_formula_can)\n",
    "                        and len(pd.read_csv(sub_sub_dirALL_formula_can, sep=\"\\t\"))\n",
    "                        > 0\n",
    "                    ):\n",
    "                        ALL_structure_csv = pd.read_csv(\n",
    "                            sub_sub_dirALL_structure_can, sep=\"\\t\"\n",
    "                        )\n",
    "                        ALL_formula_csv = pd.read_csv(\n",
    "                            sub_sub_dirALL_formula_can, sep=\"\\t\"\n",
    "                        )\n",
    "                        ALL_Canopus = pd.read_csv(ALL_Canopus_csv, sep=\"\\t\")\n",
    "                        # Add the structure and formula files together\n",
    "                        for structure, rows in ALL_structure_csv.iterrows():\n",
    "                            for formula, rows in ALL_formula_csv.iterrows():\n",
    "                                if (\n",
    "                                    ALL_structure_csv[\"formulaRank\"][structure]\n",
    "                                    == ALL_formula_csv[\"rank\"][formula]\n",
    "                                ):\n",
    "                                    ALL_structure_csv.loc[\n",
    "                                        structure, \"SiriusScore\"\n",
    "                                    ] = ALL_formula_csv[\"SiriusScore\"][formula]\n",
    "                                    ALL_structure_csv.loc[\n",
    "                                        structure, \"numExplainedPeaks\"\n",
    "                                    ] = ALL_formula_csv[\"numExplainedPeaks\"][\n",
    "                                        formula\n",
    "                                    ]\n",
    "                                    ALL_structure_csv.loc[\n",
    "                                        structure, \"explainedIntensity\"\n",
    "                                    ] = ALL_formula_csv[\"explainedIntensity\"][\n",
    "                                        formula\n",
    "                                    ]\n",
    "                                    # ALL_structure_csv.loc[structure, \"SuspectListEntry\"] = \"FALSE\"\n",
    "                                    if len(ALL_Canopus) > 0:\n",
    "                                        if (\n",
    "                                            ALL_formula_csv[\"molecularFormula\"][\n",
    "                                                formula\n",
    "                                            ]\n",
    "                                            == ALL_Canopus[\"molecularFormula\"][0]\n",
    "                                        ):\n",
    "                                            ALL_structure_csv.loc[\n",
    "                                                structure, \"superclass\"\n",
    "                                            ] = ALL_Canopus[\"superclass\"][0]\n",
    "                                            ALL_structure_csv.loc[\n",
    "                                                structure, \"class\"\n",
    "                                            ] = ALL_Canopus[\"class\"][0]\n",
    "                                            ALL_structure_csv.loc[\n",
    "                                                structure, \"subclass\"\n",
    "                                            ] = ALL_Canopus[\"subclass\"][0]\n",
    "\n",
    "#                                 for str_siriusA, row in ALL_structure_csv.iterrows():\n",
    "#                                     if not str_can_score(ALL_structure_csv, str_siriusA):\n",
    "#                                         ALL_structure_csv = ALL_structure_csv.drop(\n",
    "#                                             str_siriusA, inplace=False\n",
    "#                                         )\n",
    "\n",
    "                    result_sirius_name = (\n",
    "                        sub_dir\n",
    "                        + db\n",
    "                        + \"_results_for_\"\n",
    "                        + json_dirALL[0].split(\"_\")[-1]\n",
    "                        + \"_\"\n",
    "                        + \"structure.csv\"\n",
    "                    )\n",
    "                    msp.loc[mz, \"sirius_result_dir\"] = result_sirius_name\n",
    "\n",
    "                    ALL_structure_csv.to_csv(result_sirius_name)\n",
    "\n",
    "                elif not (\n",
    "                    os.path.exists(sub_sub_dirALL_structure_can)\n",
    "                    and len(pd.read_csv(sub_sub_dirALL_structure_can, sep=\"\\t\")) == 0\n",
    "                ):\n",
    "                    if (\n",
    "                        os.path.exists(sub_sub_dirALL_formula_can)\n",
    "                        and len(pd.read_csv(sub_sub_dirALL_formula_can, sep=\"\\t\"))\n",
    "                        > 0\n",
    "                    ):\n",
    "                        ALL_formula_csv = pd.read_csv(\n",
    "                            sub_sub_dirALL_formula_can, sep=\"\\t\"\n",
    "                        )\n",
    "                        ALL_Canopus = pd.read_csv(ALL_Canopus_csv, sep=\"\\t\")\n",
    "                        if len(ALL_Canopus) > 0:\n",
    "                            for formula, rows in ALL_formula_csv.iterrows():\n",
    "                                ALL_formula_csv.loc[\n",
    "                                    formula, \"superclass\"\n",
    "                                ] = ALL_Canopus[\"superclass\"][0]\n",
    "                                ALL_formula_csv.loc[formula, \"class\"] = ALL_Canopus[\n",
    "                                    \"class\"\n",
    "                                ][0]\n",
    "                                ALL_formula_csv.loc[\n",
    "                                    formula, \"subclass\"\n",
    "                                ] = ALL_Canopus[\"subclass\"][0]\n",
    "\n",
    "                        for for_siriusA, row in ALL_formula_csv.iterrows():\n",
    "                            if (\n",
    "                                not ALL_formula_csv[\"explainedIntensity\"][\n",
    "                                    for_siriusA\n",
    "                                ]\n",
    "                                >= exp_int\n",
    "                            ):\n",
    "                                ALL_formula_csv = ALL_formula_csv.drop(\n",
    "                                    for_siriusA, inplace=False\n",
    "                                )\n",
    "\n",
    "                        result_sirius_name = (\n",
    "                            sub_dir\n",
    "                            + db\n",
    "                            + \"_results_for_\"\n",
    "                            + json_dirALL[0].split(\"_\")[-1]\n",
    "                            + \"_\"\n",
    "                            + \"formula.csv\"\n",
    "                        )\n",
    "                        msp.loc[\n",
    "                            mz, \"sirius_result_dir\"\n",
    "                        ] = result_sirius_name\n",
    "\n",
    "                        ALL_formula_csv.to_csv(\n",
    "                            sub_dir\n",
    "                            + db\n",
    "                            + \"_results_for_\"\n",
    "                            + json_dirALL[0].split(\"_\")[-1]\n",
    "                            + \"_\"\n",
    "                            + \"formula.csv\"\n",
    "                        )\n",
    "\n",
    "                    else:\n",
    "                        print(\"no file for formula\")\n",
    "                else:\n",
    "                    print(\"no file for structure or formula\")\n",
    "        msp.to_csv(msp_csv)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 179,
   "id": "035d31ec",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['DS_201124_SC_full_PRM_pos_03',\n",
       " 'DS_201124_SC_full_PRM_pos_04',\n",
       " 'DS200309_Scost_QC_70k_neg_PRM',\n",
       " 'DS_201124_SC_full_PRM_pos_05',\n",
       " 'DS_201124_SC_full_PRM_pos_02',\n",
       " 'DS_201124_SC_full_PRM_neg_03',\n",
       " 'DS_201124_SC_full_PRM_neg_04',\n",
       " 'DS200309_Scost_QC_70k_pos_PRM',\n",
       " 'DS_201124_SC_full_PRM_neg_05',\n",
       " 'DS_201124_SC_full_PRM_neg_02',\n",
       " 'DS_201124_SC_full_PRM_neg_10',\n",
       " 'DS_201124_SC_full_PRM_pos_10',\n",
       " 'DS_201124_SC_full_PRM_pos_07',\n",
       " 'DS_201124_SC_full_PRM_pos_09',\n",
       " 'DS_201124_SC_full_PRM_pos_08',\n",
       " 'DS_201124_SC_full_PRM_pos_01',\n",
       " 'DS_201124_SC_full_PRM_pos_06',\n",
       " 'DS_201124_SC_full_PRM_neg_07',\n",
       " 'DS_201124_SC_full_PRM_neg_09',\n",
       " 'DS_201124_SC_full_PRM_neg_08',\n",
       " 'DS_201124_SC_full_PRM_neg_01',\n",
       " 'DS_201124_SC_full_PRM_neg_06']"
      ]
     },
     "execution_count": 179,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "folders2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "76ecb3ed",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3de4903f",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "25a29a41",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 177,
   "id": "4c66abb1",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "no file for formula\n",
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    {
     "name": "stdout",
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     "text": [
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      "['50_NA_iso_MS1p_159.939056396484_SIRIUS_param.json', '53_NA_iso_MS1p_258.921020507813_SIRIUS_param.json', '70_iso_MS1p_172.830642700195_SIRIUS_param.json', '58_NA_iso_MS1p_238.912902832031_SIRIUS_param.json', '59_NA_iso_MS1p_303.001861572266_SIRIUS_param.json', '10_NA_iso_NA_MS1p_672.487854003906_SIRIUS_param.json', '14_iso_MS1p_767.486450195313_SIRIUS_param.json', '49_NA_iso_MS1p_198.954238891602_SIRIUS_param.json', '13_NA_iso_MS1p_220.853302001953_SIRIUS_param.json', '7_NA_iso_NA_MS1p_575.434936523438_SIRIUS_param.json', '39_NA_iso_NA_MS1p_161.913604736328_SIRIUS_param.json', '21_NA_iso_MS1p_143.951919555664_SIRIUS_param.json', '1_NA_iso_NA_MS1p_459.064605712891_SIRIUS_param.json', '3_NA_iso_MS1p_237.911437988281_SIRIUS_param.json', '34_NA_iso_MS1p_177.903167724609_SIRIUS_param.json', '8_NA_iso_NA_MS1p_588.429931640625_SIRIUS_param.json', '6_NA_iso_NA_MS1p_491.319702148438_SIRIUS_param.json', '57_NA_iso_MS1p_255.822494506836_SIRIUS_param.json', '51_NA_iso_NA_MS1p_210.931686401367_SIRIUS_param.json', '35_iso_MS1p_226.996658325195_SIRIUS_param.json', '2_NA_iso_NA_MS1p_340.876068115234_SIRIUS_param.json', '28_NA_iso_MS1p_235.953491210938_SIRIUS_param.json', '42_NA_iso_NA_MS1p_316.779235839844_SIRIUS_param.json', '68_NA_iso_NA_MS1p_257.819427490234_SIRIUS_param.json', '31_NA_iso_NA_MS1p_198.864395141602_SIRIUS_param.json', '46_NA_iso_NA_MS1p_345.718780517578_SIRIUS_param.json', '27_NA_iso_MS1p_171.066390991211_SIRIUS_param.json', '69_NA_iso_MS1p_197.902374267578_SIRIUS_param.json', '65_NA_iso_NA_MS1p_146.966094970703_SIRIUS_param.json', '61_iso_MS1p_222.005477905273_SIRIUS_param.json', '54_NA_iso_NA_MS1p_286.912078857422_SIRIUS_param.json', '52_NA_iso_MS1p_376.856811523438_SIRIUS_param.json', '55_NA_iso_NA_MS1p_289.069793701172_SIRIUS_param.json', '64_NA_iso_NA_MS1p_146.046005249023_SIRIUS_param.json', '25_NA_iso_MS1p_187.941879272461_SIRIUS_param.json', '5_NA_iso_NA_MS1p_435.855743408203_SIRIUS_param.json', '63_NA_iso_MS1p_322.069030761719_SIRIUS_param.json', '32_NA_iso_NA_MS1p_314.784698486328_SIRIUS_param.json', '37_NA_iso_NA_MS1p_586.315185546875_SIRIUS_param.json', '26_NA_iso_NA_MS1p_150.915573120117_SIRIUS_param.json', '20_iso_MS1p_234.921569824219_SIRIUS_param.json', '38_NA_iso_NA_MS1p_536.299682617188_SIRIUS_param.json', '66_NA_iso_NA_MS1p_102.95694732666_SIRIUS_param.json', '60_NA_iso_MS1p_182.043594360352_SIRIUS_param.json', '43_NA_iso_NA_MS1p_125.928810119629_SIRIUS_param.json', '45_NA_iso_NA_MS1p_369.763732910156_SIRIUS_param.json', '15_NA_iso_MS1p_453.225891113281_SIRIUS_param.json', '4_NA_iso_NA_MS1p_388.841735839844_SIRIUS_param.json', '9_NA_iso_NA_MS1p_315.833709716797_SIRIUS_param.json', '41_NA_iso_NA_MS1p_294.831237792969_SIRIUS_param.json', '36_NA_iso_MS1p_272.883331298828_SIRIUS_param.json', '56_NA_iso_NA_MS1p_386.939453125_SIRIUS_param.json', '22_iso_MS1p_773.533935546875_SIRIUS_param.json', '47_NA_iso_NA_MS1p_375.604736328125_SIRIUS_param.json', '12_NA_iso_MS1p_691.455688476563_SIRIUS_param.json', '18_NA_iso_MS1p_703.262084960938_SIRIUS_param.json', '23_NA_iso_MS1p_144.923446655273_SIRIUS_param.json', '44_NA_iso_NA_MS1p_301.683227539063_SIRIUS_param.json', '33_iso_MS1p_294.831085205078_SIRIUS_param.json', '17_NA_iso_MS1p_315.196868896484_SIRIUS_param.json', '19_iso_MS1p_297.170989990234_SIRIUS_param.json', '67_NA_iso_NA_MS1p_129.975723266602_SIRIUS_param.json', '29_NA_iso_MS1p_350.860473632813_SIRIUS_param.json', '48_NA_iso_NA_MS1p_218.896179199219_SIRIUS_param.json', '62_NA_iso_NA_MS1p_305.123474121094_SIRIUS_param.json', '11_NA_iso_MS1p_335.902221679688_SIRIUS_param.json', '30_NA_iso_MS1p_272.883483886719_SIRIUS_param.json', '16_NA_iso_NA_MS1p_213.880157470703_SIRIUS_param.json', '40_NA_iso_NA_MS1p_94.980812072754_SIRIUS_param.json', '24_NA_iso_NA_MS1p_201.957595825195_SIRIUS_param.json']\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for formula\n",
      "['38_NA_iso_NA_MS1p_201.906127929688_SIRIUS_param.json', '35_NA_iso_NA_MS1p_254.07063293457_SIRIUS_param.json', '50_NA_iso_NA_MS1p_160.935470581055_SIRIUS_param.json', '11_NA_iso_NA_MS1p_553.269226074219_SIRIUS_param.json', '46_NA_iso_MS1p_315.833618164063_SIRIUS_param.json', '45_NA_iso_NA_MS1p_278.769378662109_SIRIUS_param.json', '68_NA_iso_NA_MS1p_96.960182189941_SIRIUS_param.json', '31_NA_iso_NA_MS1p_174.964248657227_SIRIUS_param.json', '58_NA_iso_NA_MS1p_232.853866577148_SIRIUS_param.json', '7_NA_iso_MS1p_759.435607910156_SIRIUS_param.json', '47_NA_iso_NA_MS1p_248.741088867188_SIRIUS_param.json', '41_NA_iso_NA_MS1p_208.934646606445_SIRIUS_param.json', '28_NA_iso_NA_MS1p_364.889129638672_SIRIUS_param.json', '64_NA_iso_NA_MS1p_411.056427001953_SIRIUS_param.json', '2_NA_iso_MS1p_115.920883178711_SIRIUS_param.json', '25_NA_iso_NA_MS1p_316.779052734375_SIRIUS_param.json', '22_NA_iso_NA_MS1p_529.265625_SIRIUS_param.json', '37_NA_iso_NA_MS1p_564.330871582031_SIRIUS_param.json', '1_NA_iso_NA_MS1p_458.061157226563_SIRIUS_param.json', '34_NA_iso_NA_MS1p_231.931884765625_SIRIUS_param.json', '32_NA_iso_NA_MS1p_199.850982666016_SIRIUS_param.json', '48_iso_MS1p_317.830474853516_SIRIUS_param.json', '70_NA_iso_MS1p_275.905883789063_SIRIUS_param.json', '60_NA_iso_NA_MS1p_278.9814453125_SIRIUS_param.json', '57_NA_iso_MS1p_152.995697021484_SIRIUS_param.json', '65_iso_MS1p_129.975723266602_SIRIUS_param.json', '39_NA_iso_NA_MS1p_234.82014465332_SIRIUS_param.json', '10_NA_iso_MS1p_140.986145019531_SIRIUS_param.json', '61_NA_iso_NA_MS1p_377.085876464844_SIRIUS_param.json', '56_NA_iso_MS1p_94.925132751465_SIRIUS_param.json', '52_NA_iso_MS1p_213.879959106445_SIRIUS_param.json', '53_NA_iso_MS1p_222.900833129883_SIRIUS_param.json', '62_iso_MS1p_167.013122558594_SIRIUS_param.json', '5_NA_iso_MS1p_309.174407958984_SIRIUS_param.json', '19_NA_iso_NA_MS1p_475.182739257813_SIRIUS_param.json', '29_NA_iso_MS1p_273.883361816406_SIRIUS_param.json', '24_NA_iso_NA_MS1p_315.833465576172_SIRIUS_param.json', '49_NA_iso_MS1p_212.960632324219_SIRIUS_param.json', '63_NA_iso_NA_MS1p_146.046081542969_SIRIUS_param.json', '9_NA_iso_NA_MS1p_238.915878295898_SIRIUS_param.json', '42_NA_iso_MS1p_252.884490966797_SIRIUS_param.json', '54_NA_iso_MS1p_396.865081787109_SIRIUS_param.json', '20_NA_iso_NA_MS1p_761.451416015625_SIRIUS_param.json', '44_NA_iso_NA_MS1p_178.844131469727_SIRIUS_param.json', '66_NA_iso_NA_MS1p_119.946998596191_SIRIUS_param.json', '71_NA_iso_NA_MS1p_434.871765136719_SIRIUS_param.json', '59_NA_iso_MS1p_299.098571777344_SIRIUS_param.json', '51_NA_iso_NA_MS1p_271.059143066406_SIRIUS_param.json', '43_NA_iso_NA_MS1p_301.769256591797_SIRIUS_param.json', '17_NA_iso_NA_MS1p_357.228515625_SIRIUS_param.json', '40_NA_iso_NA_MS1p_267.065826416016_SIRIUS_param.json', '13_NA_iso_MS1p_481.257354736328_SIRIUS_param.json', '23_NA_iso_NA_MS1p_443.841674804688_SIRIUS_param.json', '69_NA_iso_MS1p_304.908721923828_SIRIUS_param.json', '14_NA_iso_MS1p_240.911071777344_SIRIUS_param.json', '4_NA_iso_NA_MS1p_315.833435058594_SIRIUS_param.json', '18_NA_iso_NA_MS1p_221.154724121094_SIRIUS_param.json', '3_NA_iso_NA_MS1p_150.915603637695_SIRIUS_param.json', '8_NA_iso_NA_MS1p_602.445861816406_SIRIUS_param.json', '33_NA_iso_MS1p_241.012252807617_SIRIUS_param.json', '12_NA_iso_MS1p_172.957809448242_SIRIUS_param.json', '16_NA_iso_NA_MS1p_273.186279296875_SIRIUS_param.json', '30_NA_iso_NA_MS1p_232.825469970703_SIRIUS_param.json', '15_NA_iso_NA_MS1p_327.233154296875_SIRIUS_param.json', '27_NA_iso_MS1p_474.842559814453_SIRIUS_param.json', '26_NA_iso_MS1p_367.862884521484_SIRIUS_param.json', '21_NA_iso_NA_MS1p_229.937255859375_SIRIUS_param.json', '67_NA_iso_NA_MS1p_146.966125488281_SIRIUS_param.json']\n",
      "no file for formula\n",
      "no file for structure or formula\n"
     ]
    },
    {
     "ename": "IndexError",
     "evalue": "list index out of range",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mIndexError\u001b[0m                                Traceback (most recent call last)",
      "Input \u001b[0;32mIn [177]\u001b[0m, in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      7\u001b[0m \u001b[38;5;28mprint\u001b[39m(foldersir)\n\u001b[1;32m      8\u001b[0m sirius_dirs \u001b[38;5;241m=\u001b[39m foldersir\n\u001b[0;32m----> 9\u001b[0m \u001b[43msirius_postproc\u001b[49m\u001b[43m(\u001b[49m\u001b[43mentry\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msirius_dirs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdb\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mALL\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n",
      "Input \u001b[0;32mIn [165]\u001b[0m, in \u001b[0;36msirius_postproc\u001b[0;34m(entry, sirius_dirs, db)\u001b[0m\n\u001b[1;32m     18\u001b[0m         files_for_mz\u001b[38;5;241m.\u001b[39mappend(file)\n\u001b[1;32m     20\u001b[0m \u001b[38;5;66;03m# extract the formula and structure files\u001b[39;00m\n\u001b[0;32m---> 21\u001b[0m json_dirALL \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mnext\u001b[39m(os\u001b[38;5;241m.\u001b[39mwalk(sub_dir \u001b[38;5;241m+\u001b[39m \u001b[43mfiles_for_mz\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m))[\u001b[38;5;241m1\u001b[39m]\n\u001b[1;32m     23\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(json_dirALL) \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[1;32m     24\u001b[0m     sub_sub_dirALL_structure_can \u001b[38;5;241m=\u001b[39m (sub_dir \u001b[38;5;241m+\u001b[39m\n\u001b[1;32m     25\u001b[0m         files_for_mz[\u001b[38;5;241m0\u001b[39m]\n\u001b[1;32m     26\u001b[0m         \u001b[38;5;241m+\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m     27\u001b[0m         \u001b[38;5;241m+\u001b[39m json_dirALL[\u001b[38;5;241m0\u001b[39m]\n\u001b[1;32m     28\u001b[0m         \u001b[38;5;241m+\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/structure_candidates.tsv\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m     29\u001b[0m     )\n",
      "\u001b[0;31mIndexError\u001b[0m: list index out of range"
     ]
    }
   ],
   "source": [
    "for i in folders2:\n",
    "    entry = path + \"/\" + i\n",
    "    sub_dir = entry + \"/insilico/SIRIUS/\"\n",
    "    file = os.listdir(sub_dir)\n",
    "    foldersir = [x for x in os.listdir(sub_dir) if x.endswith('.json')]\n",
    "    foldersir = [x for x in foldersir if not 'SList.json' in x]\n",
    "    #print(foldersir)\n",
    "    sirius_dirs = foldersir\n",
    "    sirius_postproc(entry, sirius_dirs, db = \"ALL\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 191,
   "id": "9c1f08f7",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/Users/mahnoorzulfiqar/OneDriveUNI/MAW-Diatom/SmarinoiRun1/DS_201124_SC_full_PRM_neg_06'"
      ]
     },
     "execution_count": 191,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "entry"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 193,
   "id": "c133de37",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['38_NA_iso_NA_MS1p_201.906127929688_SIRIUS_param.json', '35_NA_iso_NA_MS1p_254.07063293457_SIRIUS_param.json', '50_NA_iso_NA_MS1p_160.935470581055_SIRIUS_param.json', '11_NA_iso_NA_MS1p_553.269226074219_SIRIUS_param.json', '46_NA_iso_MS1p_315.833618164063_SIRIUS_param.json', '45_NA_iso_NA_MS1p_278.769378662109_SIRIUS_param.json', '68_NA_iso_NA_MS1p_96.960182189941_SIRIUS_param.json', '31_NA_iso_NA_MS1p_174.964248657227_SIRIUS_param.json', '58_NA_iso_NA_MS1p_232.853866577148_SIRIUS_param.json', '7_NA_iso_MS1p_759.435607910156_SIRIUS_param.json', '47_NA_iso_NA_MS1p_248.741088867188_SIRIUS_param.json', '41_NA_iso_NA_MS1p_208.934646606445_SIRIUS_param.json', '28_NA_iso_NA_MS1p_364.889129638672_SIRIUS_param.json', '64_NA_iso_NA_MS1p_411.056427001953_SIRIUS_param.json', '2_NA_iso_MS1p_115.920883178711_SIRIUS_param.json', '25_NA_iso_NA_MS1p_316.779052734375_SIRIUS_param.json', '22_NA_iso_NA_MS1p_529.265625_SIRIUS_param.json', '37_NA_iso_NA_MS1p_564.330871582031_SIRIUS_param.json', '1_NA_iso_NA_MS1p_458.061157226563_SIRIUS_param.json', '34_NA_iso_NA_MS1p_231.931884765625_SIRIUS_param.json', '32_NA_iso_NA_MS1p_199.850982666016_SIRIUS_param.json', '48_iso_MS1p_317.830474853516_SIRIUS_param.json', '70_NA_iso_MS1p_275.905883789063_SIRIUS_param.json', '60_NA_iso_NA_MS1p_278.9814453125_SIRIUS_param.json', '57_NA_iso_MS1p_152.995697021484_SIRIUS_param.json', '65_iso_MS1p_129.975723266602_SIRIUS_param.json', '39_NA_iso_NA_MS1p_234.82014465332_SIRIUS_param.json', '10_NA_iso_MS1p_140.986145019531_SIRIUS_param.json', '61_NA_iso_NA_MS1p_377.085876464844_SIRIUS_param.json', '56_NA_iso_MS1p_94.925132751465_SIRIUS_param.json', '52_NA_iso_MS1p_213.879959106445_SIRIUS_param.json', '53_NA_iso_MS1p_222.900833129883_SIRIUS_param.json', '62_iso_MS1p_167.013122558594_SIRIUS_param.json', '5_NA_iso_MS1p_309.174407958984_SIRIUS_param.json', '19_NA_iso_NA_MS1p_475.182739257813_SIRIUS_param.json', '29_NA_iso_MS1p_273.883361816406_SIRIUS_param.json', '24_NA_iso_NA_MS1p_315.833465576172_SIRIUS_param.json', '49_NA_iso_MS1p_212.960632324219_SIRIUS_param.json', '63_NA_iso_NA_MS1p_146.046081542969_SIRIUS_param.json', '9_NA_iso_NA_MS1p_238.915878295898_SIRIUS_param.json', '42_NA_iso_MS1p_252.884490966797_SIRIUS_param.json', '54_NA_iso_MS1p_396.865081787109_SIRIUS_param.json', '20_NA_iso_NA_MS1p_761.451416015625_SIRIUS_param.json', '44_NA_iso_NA_MS1p_178.844131469727_SIRIUS_param.json', '66_NA_iso_NA_MS1p_119.946998596191_SIRIUS_param.json', '71_NA_iso_NA_MS1p_434.871765136719_SIRIUS_param.json', '59_NA_iso_MS1p_299.098571777344_SIRIUS_param.json', '51_NA_iso_NA_MS1p_271.059143066406_SIRIUS_param.json', '43_NA_iso_NA_MS1p_301.769256591797_SIRIUS_param.json', '17_NA_iso_NA_MS1p_357.228515625_SIRIUS_param.json', '40_NA_iso_NA_MS1p_267.065826416016_SIRIUS_param.json', '13_NA_iso_MS1p_481.257354736328_SIRIUS_param.json', '23_NA_iso_NA_MS1p_443.841674804688_SIRIUS_param.json', '69_NA_iso_MS1p_304.908721923828_SIRIUS_param.json', '14_NA_iso_MS1p_240.911071777344_SIRIUS_param.json', '4_NA_iso_NA_MS1p_315.833435058594_SIRIUS_param.json', '18_NA_iso_NA_MS1p_221.154724121094_SIRIUS_param.json', '3_NA_iso_NA_MS1p_150.915603637695_SIRIUS_param.json', '8_NA_iso_NA_MS1p_602.445861816406_SIRIUS_param.json', '33_NA_iso_MS1p_241.012252807617_SIRIUS_param.json', '12_NA_iso_MS1p_172.957809448242_SIRIUS_param.json', '16_NA_iso_NA_MS1p_273.186279296875_SIRIUS_param.json', '30_NA_iso_NA_MS1p_232.825469970703_SIRIUS_param.json', '15_NA_iso_NA_MS1p_327.233154296875_SIRIUS_param.json', '27_NA_iso_MS1p_474.842559814453_SIRIUS_param.json', '26_NA_iso_MS1p_367.862884521484_SIRIUS_param.json', '21_NA_iso_NA_MS1p_229.937255859375_SIRIUS_param.json', '67_NA_iso_NA_MS1p_146.966125488281_SIRIUS_param.json']\n"
     ]
    }
   ],
   "source": [
    "sub_dir = entry + \"/insilico/SIRIUS/\"\n",
    "file = os.listdir(sub_dir)\n",
    "foldersir = [x for x in os.listdir(sub_dir) if x.endswith('.json')]\n",
    "foldersir = [x for x in foldersir if not 'SList.json' in x]\n",
    "#print(foldersir)\n",
    "sirius_dirs = foldersir\n",
    "print(sirius_dirs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 194,
   "id": "04b7ba47",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "no file for formula\n",
      "no file for structure or formula\n",
      "no file for formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n",
      "no file for structure or formula\n"
     ]
    }
   ],
   "source": [
    "sirius_postproc(entry, sirius_dirs, db = \"ALL\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 190,
   "id": "33d74425",
   "metadata": {},
   "outputs": [],
   "source": [
    "def sirius_postproc(entry, sirius_dirs, db):\n",
    "    if os.path.isdir(entry + \"/insilico/SIRIUS/\"):\n",
    "        sub_dir = entry + \"/insilico/SIRIUS/\"\n",
    "        msp_csv = entry + \"/insilico/MS1DATA.csv\"\n",
    "        if os.path.exists(msp_csv) and os.path.exists(sub_dir):\n",
    "            # output json files from SIRIUS\n",
    "            files_S = sirius_dirs\n",
    "            # list of precursor m/z\n",
    "            msp = pd.read_csv(msp_csv)\n",
    "\n",
    "            # for each mz\n",
    "            for mz, row in msp.iterrows():\n",
    "                # make a list of files with this mz\n",
    "                files_for_mz = []\n",
    "\n",
    "                for file in files_S:\n",
    "                    if str(msp[\"premz\"][mz]) in file:\n",
    "                        files_for_mz.append(file)\n",
    "                if len(files_for_mz) > 0:\n",
    "                    # extract the formula and structure files\n",
    "                    json_dirALL = next(os.walk(sub_dir + files_for_mz[0]))[1]\n",
    "\n",
    "                    if len(json_dirALL) == 1:\n",
    "                        sub_sub_dirALL_structure_can = (sub_dir +\n",
    "                            files_for_mz[0]\n",
    "                            + \"/\"\n",
    "                            + json_dirALL[0]\n",
    "                            + \"/structure_candidates.tsv\"\n",
    "                        )\n",
    "                        sub_sub_dirALL_formula_can = (sub_dir +\n",
    "                            files_for_mz[0]\n",
    "                            + \"/\"\n",
    "                            + json_dirALL[0]\n",
    "                            + \"/formula_candidates.tsv\"\n",
    "                        )\n",
    "                        ALL_Canopus_csv = sub_dir + files_for_mz[0] + \"/canopus_summary.tsv\"\n",
    "\n",
    "                        # if both structure files exist\n",
    "                        if (\n",
    "                            os.path.exists(sub_sub_dirALL_structure_can)\n",
    "                            and len(pd.read_csv(sub_sub_dirALL_structure_can, sep=\"\\t\")) > 0\n",
    "                        ):\n",
    "                            if (\n",
    "                                 os.path.exists(sub_sub_dirALL_formula_can)\n",
    "                                and len(pd.read_csv(sub_sub_dirALL_formula_can, sep=\"\\t\"))\n",
    "                                > 0\n",
    "                            ):\n",
    "                                ALL_structure_csv = pd.read_csv(\n",
    "                                    sub_sub_dirALL_structure_can, sep=\"\\t\"\n",
    "                                )\n",
    "                                ALL_formula_csv = pd.read_csv(\n",
    "                                    sub_sub_dirALL_formula_can, sep=\"\\t\"\n",
    "                                )\n",
    "                                ALL_Canopus = pd.read_csv(ALL_Canopus_csv, sep=\"\\t\")\n",
    "                                # Add the structure and formula files together\n",
    "                                for structure, rows in ALL_structure_csv.iterrows():\n",
    "                                    for formula, rows in ALL_formula_csv.iterrows():\n",
    "                                        if (\n",
    "                                            ALL_structure_csv[\"formulaRank\"][structure]\n",
    "                                            == ALL_formula_csv[\"rank\"][formula]\n",
    "                                        ):\n",
    "                                            ALL_structure_csv.loc[\n",
    "                                                structure, \"SiriusScore\"\n",
    "                                            ] = ALL_formula_csv[\"SiriusScore\"][formula]\n",
    "                                            ALL_structure_csv.loc[\n",
    "                                                structure, \"numExplainedPeaks\"\n",
    "                                            ] = ALL_formula_csv[\"numExplainedPeaks\"][\n",
    "                                                formula\n",
    "                                            ]\n",
    "                                            ALL_structure_csv.loc[\n",
    "                                                structure, \"explainedIntensity\"\n",
    "                                            ] = ALL_formula_csv[\"explainedIntensity\"][\n",
    "                                                formula\n",
    "                                            ]\n",
    "                                            # ALL_structure_csv.loc[structure, \"SuspectListEntry\"] = \"FALSE\"\n",
    "                                            if len(ALL_Canopus) > 0:\n",
    "                                                if (\n",
    "                                                    ALL_formula_csv[\"molecularFormula\"][\n",
    "                                                        formula\n",
    "                                                    ]\n",
    "                                                    == ALL_Canopus[\"molecularFormula\"][0]\n",
    "                                                ):\n",
    "                                                    ALL_structure_csv.loc[\n",
    "                                                        structure, \"superclass\"\n",
    "                                                    ] = ALL_Canopus[\"superclass\"][0]\n",
    "                                                    ALL_structure_csv.loc[\n",
    "                                                        structure, \"class\"\n",
    "                                                    ] = ALL_Canopus[\"class\"][0]\n",
    "                                                    ALL_structure_csv.loc[\n",
    "                                                        structure, \"subclass\"\n",
    "                                                    ] = ALL_Canopus[\"subclass\"][0]\n",
    "\n",
    "    #                                 for str_siriusA, row in ALL_structure_csv.iterrows():\n",
    "    #                                     if not str_can_score(ALL_structure_csv, str_siriusA):\n",
    "    #                                         ALL_structure_csv = ALL_structure_csv.drop(\n",
    "    #                                             str_siriusA, inplace=False\n",
    "    #                                         )\n",
    "\n",
    "                            result_sirius_name = (\n",
    "                                sub_dir\n",
    "                                + db\n",
    "                                + \"_results_for_\"\n",
    "                                + json_dirALL[0].split(\"_\")[-1]\n",
    "                                + \"_\"\n",
    "                                + \"structure.csv\"\n",
    "                            )\n",
    "                            msp.loc[mz, \"sirius_result_dir\"] = result_sirius_name\n",
    "\n",
    "                            ALL_structure_csv.to_csv(result_sirius_name)\n",
    "\n",
    "                        elif not (\n",
    "                            os.path.exists(sub_sub_dirALL_structure_can)\n",
    "                            and len(pd.read_csv(sub_sub_dirALL_structure_can, sep=\"\\t\")) == 0\n",
    "                        ):\n",
    "                            if (\n",
    "                                os.path.exists(sub_sub_dirALL_formula_can)\n",
    "                                and len(pd.read_csv(sub_sub_dirALL_formula_can, sep=\"\\t\"))\n",
    "                                > 0\n",
    "                            ):\n",
    "                                ALL_formula_csv = pd.read_csv(\n",
    "                                    sub_sub_dirALL_formula_can, sep=\"\\t\"\n",
    "                                )\n",
    "                                ALL_Canopus = pd.read_csv(ALL_Canopus_csv, sep=\"\\t\")\n",
    "                                if len(ALL_Canopus) > 0:\n",
    "                                    for formula, rows in ALL_formula_csv.iterrows():\n",
    "                                        ALL_formula_csv.loc[\n",
    "                                            formula, \"superclass\"\n",
    "                                        ] = ALL_Canopus[\"superclass\"][0]\n",
    "                                        ALL_formula_csv.loc[formula, \"class\"] = ALL_Canopus[\n",
    "                                            \"class\"\n",
    "                                        ][0]\n",
    "                                        ALL_formula_csv.loc[\n",
    "                                            formula, \"subclass\"\n",
    "                                        ] = ALL_Canopus[\"subclass\"][0]\n",
    "\n",
    "                                for for_siriusA, row in ALL_formula_csv.iterrows():\n",
    "                                    if (\n",
    "                                        not ALL_formula_csv[\"explainedIntensity\"][\n",
    "                                            for_siriusA\n",
    "                                        ]\n",
    "                                        >= exp_int\n",
    "                                    ):\n",
    "                                        ALL_formula_csv = ALL_formula_csv.drop(\n",
    "                                            for_siriusA, inplace=False\n",
    "                                        )\n",
    "\n",
    "                                result_sirius_name = (\n",
    "                                    sub_dir\n",
    "                                    + db\n",
    "                                    + \"_results_for_\"\n",
    "                                    + json_dirALL[0].split(\"_\")[-1]\n",
    "                                    + \"_\"\n",
    "                                    + \"formula.csv\"\n",
    "                                )\n",
    "                                msp.loc[\n",
    "                                    mz, \"sirius_result_dir\"\n",
    "                                ] = result_sirius_name\n",
    "\n",
    "                                ALL_formula_csv.to_csv(\n",
    "                                    sub_dir\n",
    "                                    + db\n",
    "                                    + \"_results_for_\"\n",
    "                                    + json_dirALL[0].split(\"_\")[-1]\n",
    "                                    + \"_\"\n",
    "                                    + \"formula.csv\"\n",
    "                                )\n",
    "\n",
    "                            else:\n",
    "                                print(\"no file for formula\")\n",
    "                        else:\n",
    "                            print(\"no file for structure or formula\")\n",
    "            msp.to_csv(msp_csv)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9c97791a",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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