{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Translate spectral libraries\n",
    "\n",
    "AlphaBase/PeptDeep to TSV (DiaNN/Spectronaut/OpenSWATH)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "python"
    }
   },
   "outputs": [],
   "source": [
    "#%pip install peptdeep"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "python"
    }
   },
   "outputs": [],
   "source": [
    "%reload_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "python"
    }
   },
   "outputs": [],
   "source": [
    "alphapeptdeep_hdf = r'y:\\User\\Feng\\speclib\\human_swissprot.speclib.hdf'\n",
    "top_k_frag = 16"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Do not change below"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "python"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'y:\\\\User\\\\Feng\\\\speclib\\\\human_swissprot_frags=16.speclib.tsv'"
      ]
     },
     "execution_count": null,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "frag_inten = 0.001\n",
    "\n",
    "\n",
    "min_frag_mz = 200\n",
    "min_frag_nAA = 0\n",
    "\n",
    "output_diann_tsv = (\n",
    "    f\"{alphapeptdeep_hdf[:-len('.speclib.hdf')]}_frags={top_k_frag}.speclib.tsv\"\n",
    ")\n",
    "output_diann_tsv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "python"
    }
   },
   "outputs": [],
   "source": [
    "from peptdeep.protein.fasta import PredictSpecLibFasta\n",
    "\n",
    "fasta_lib = PredictSpecLibFasta(\n",
    "    None, \n",
    "    decoy=None\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "python"
    }
   },
   "outputs": [],
   "source": [
    "fasta_lib.load_hdf(alphapeptdeep_hdf, load_mod_seq=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "python"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "    }\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>description</th>\n",
       "      <th>full_name</th>\n",
       "      <th>gene_name</th>\n",
       "      <th>protein_id</th>\n",
       "      <th>sequence</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>sp|Q9H9K5|MER34_HUMAN Endogenous retroviral en...</td>\n",
       "      <td>sp|Q9H9K5|MER34_HUMAN</td>\n",
       "      <td>ERVMER34-1</td>\n",
       "      <td>Q9H9K5</td>\n",
       "      <td>MGSLSNYALLQLTLTAFLTILVQPQHLLAPVFRTLSILTNQSNCWL...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>sp|P04439|HLAA_HUMAN HLA class I histocompatib...</td>\n",
       "      <td>sp|P04439|HLAA_HUMAN</td>\n",
       "      <td>HLA-A</td>\n",
       "      <td>P04439</td>\n",
       "      <td>MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRF...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>sp|P01911|DRB1_HUMAN HLA class II histocompati...</td>\n",
       "      <td>sp|P01911|DRB1_HUMAN</td>\n",
       "      <td>HLA-DRB1</td>\n",
       "      <td>P01911</td>\n",
       "      <td>MVCLKLPGGSCMTALTVTLMVLSSPLALSGDTRPRFLWQPKRECHF...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>sp|P01889|HLAB_HUMAN HLA class I histocompatib...</td>\n",
       "      <td>sp|P01889|HLAB_HUMAN</td>\n",
       "      <td>HLA-B</td>\n",
       "      <td>P01889</td>\n",
       "      <td>MLVMAPRTVLLLLSAALALTETWAGSHSMRYFYTSVSRPGRGEPRF...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>sp|P31689|DNJA1_HUMAN DnaJ homolog subfamily A...</td>\n",
       "      <td>sp|P31689|DNJA1_HUMAN</td>\n",
       "      <td>DNAJA1</td>\n",
       "      <td>P31689</td>\n",
       "      <td>MVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFK...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>20391</th>\n",
       "      <td>sp|Q8WVZ7|RN133_HUMAN E3 ubiquitin-protein lig...</td>\n",
       "      <td>sp|Q8WVZ7|RN133_HUMAN</td>\n",
       "      <td>RNF133</td>\n",
       "      <td>Q8WVZ7</td>\n",
       "      <td>MHLLKVGTWRNNTASSWLMKFSVLWLVSQNCCRASVVWMAYMNISF...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20392</th>\n",
       "      <td>sp|P05387|RLA2_HUMAN 60S acidic ribosomal prot...</td>\n",
       "      <td>sp|P05387|RLA2_HUMAN</td>\n",
       "      <td>RPLP2</td>\n",
       "      <td>P05387</td>\n",
       "      <td>MRYVASYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISEL...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20393</th>\n",
       "      <td>sp|P51991|ROA3_HUMAN Heterogeneous nuclear rib...</td>\n",
       "      <td>sp|P51991|ROA3_HUMAN</td>\n",
       "      <td>HNRNPA3</td>\n",
       "      <td>P51991</td>\n",
       "      <td>MEVKPPPGRPQPDSGRRRRRRGEEGHDPKEPEQLRKLFIGGLSFET...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20394</th>\n",
       "      <td>sp|Q9BZX4|ROP1B_HUMAN Ropporin-1B OS=Homo sapi...</td>\n",
       "      <td>sp|Q9BZX4|ROP1B_HUMAN</td>\n",
       "      <td>ROPN1B</td>\n",
       "      <td>Q9BZX4</td>\n",
       "      <td>MAQTDKPTCIPPELPKMLKEFAKAAIRAQPQDLIQWGADYFEALSR...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20395</th>\n",
       "      <td>sp|P34096|RNAS4_HUMAN Ribonuclease 4 OS=Homo s...</td>\n",
       "      <td>sp|P34096|RNAS4_HUMAN</td>\n",
       "      <td>RNASE4</td>\n",
       "      <td>P34096</td>\n",
       "      <td>MALQRTHSLLLLLLLTLLGLGLVQPSYGQDGMYQRFLRQHVHPEET...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20396 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                             description  \\\n",
       "0      sp|Q9H9K5|MER34_HUMAN Endogenous retroviral en...   \n",
       "1      sp|P04439|HLAA_HUMAN HLA class I histocompatib...   \n",
       "2      sp|P01911|DRB1_HUMAN HLA class II histocompati...   \n",
       "3      sp|P01889|HLAB_HUMAN HLA class I histocompatib...   \n",
       "4      sp|P31689|DNJA1_HUMAN DnaJ homolog subfamily A...   \n",
       "...                                                  ...   \n",
       "20391  sp|Q8WVZ7|RN133_HUMAN E3 ubiquitin-protein lig...   \n",
       "20392  sp|P05387|RLA2_HUMAN 60S acidic ribosomal prot...   \n",
       "20393  sp|P51991|ROA3_HUMAN Heterogeneous nuclear rib...   \n",
       "20394  sp|Q9BZX4|ROP1B_HUMAN Ropporin-1B OS=Homo sapi...   \n",
       "20395  sp|P34096|RNAS4_HUMAN Ribonuclease 4 OS=Homo s...   \n",
       "\n",
       "                   full_name   gene_name protein_id  \\\n",
       "0      sp|Q9H9K5|MER34_HUMAN  ERVMER34-1     Q9H9K5   \n",
       "1       sp|P04439|HLAA_HUMAN       HLA-A     P04439   \n",
       "2       sp|P01911|DRB1_HUMAN    HLA-DRB1     P01911   \n",
       "3       sp|P01889|HLAB_HUMAN       HLA-B     P01889   \n",
       "4      sp|P31689|DNJA1_HUMAN      DNAJA1     P31689   \n",
       "...                      ...         ...        ...   \n",
       "20391  sp|Q8WVZ7|RN133_HUMAN      RNF133     Q8WVZ7   \n",
       "20392   sp|P05387|RLA2_HUMAN       RPLP2     P05387   \n",
       "20393   sp|P51991|ROA3_HUMAN     HNRNPA3     P51991   \n",
       "20394  sp|Q9BZX4|ROP1B_HUMAN      ROPN1B     Q9BZX4   \n",
       "20395  sp|P34096|RNAS4_HUMAN      RNASE4     P34096   \n",
       "\n",
       "                                                sequence  \n",
       "0      MGSLSNYALLQLTLTAFLTILVQPQHLLAPVFRTLSILTNQSNCWL...  \n",
       "1      MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRF...  \n",
       "2      MVCLKLPGGSCMTALTVTLMVLSSPLALSGDTRPRFLWQPKRECHF...  \n",
       "3      MLVMAPRTVLLLLSAALALTETWAGSHSMRYFYTSVSRPGRGEPRF...  \n",
       "4      MVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFK...  \n",
       "...                                                  ...  \n",
       "20391  MHLLKVGTWRNNTASSWLMKFSVLWLVSQNCCRASVVWMAYMNISF...  \n",
       "20392  MRYVASYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISEL...  \n",
       "20393  MEVKPPPGRPQPDSGRRRRRRGEEGHDPKEPEQLRKLFIGGLSFET...  \n",
       "20394  MAQTDKPTCIPPELPKMLKEFAKAAIRAQPQDLIQWGADYFEALSR...  \n",
       "20395  MALQRTHSLLLLLLLTLLGLGLVQPSYGQDGMYQRFLRQHVHPEET...  \n",
       "\n",
       "[20396 rows x 5 columns]"
      ]
     },
     "execution_count": null,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fasta_lib.protein_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "python"
    }
   },
   "outputs": [
    {
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       "      <td>timsTOF</td>\n",
       "      <td>-27.677099</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
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       "      <td>122.352159</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>30</td>\n",
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       "      <td>35</td>\n",
       "      <td>1159.967730</td>\n",
       "      <td>...</td>\n",
       "      <td>0.826977</td>\n",
       "      <td>timsTOF</td>\n",
       "      <td>121.377815</td>\n",
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       "      <td>False</td>\n",
       "      <td>17</td>\n",
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       "      <th>3654204</th>\n",
       "      <td>892.459656</td>\n",
       "      <td>4</td>\n",
       "      <td>60404934</td>\n",
       "      <td>60404900</td>\n",
       "      <td>1</td>\n",
       "      <td>1.109729</td>\n",
       "      <td>-1485306056792248107</td>\n",
       "      <td>-1485306056792248111</td>\n",
       "      <td>35</td>\n",
       "      <td>870.227616</td>\n",
       "      <td>...</td>\n",
       "      <td>0.826977</td>\n",
       "      <td>timsTOF</td>\n",
       "      <td>121.377815</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>17</td>\n",
       "      <td>Oxidation@M</td>\n",
       "      <td>30</td>\n",
       "      <td>978</td>\n",
       "      <td>NLTYVRGSVGPATSTLMFVAGVVGNGLALGILSAR</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3654205</th>\n",
       "      <td>791.322266</td>\n",
       "      <td>4</td>\n",
       "      <td>60404968</td>\n",
       "      <td>60404934</td>\n",
       "      <td>1</td>\n",
       "      <td>0.984398</td>\n",
       "      <td>5191231126132273755</td>\n",
       "      <td>5191231126132273751</td>\n",
       "      <td>35</td>\n",
       "      <td>976.910866</td>\n",
       "      <td>...</td>\n",
       "      <td>0.670129</td>\n",
       "      <td>timsTOF</td>\n",
       "      <td>86.427514</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>30</td>\n",
       "      <td>2299</td>\n",
       "      <td>KNQAADDDDEDLNDTNYDEFNGYAGSLFSSGPYEK</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3654206</th>\n",
       "      <td>823.819214</td>\n",
       "      <td>4</td>\n",
       "      <td>60405002</td>\n",
       "      <td>60404968</td>\n",
       "      <td>1</td>\n",
       "      <td>1.024754</td>\n",
       "      <td>-7707559913944666934</td>\n",
       "      <td>-7707559913944666938</td>\n",
       "      <td>35</td>\n",
       "      <td>958.434460</td>\n",
       "      <td>...</td>\n",
       "      <td>0.725150</td>\n",
       "      <td>timsTOF</td>\n",
       "      <td>98.687774</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>24</td>\n",
       "      <td>Carbamidomethyl@C</td>\n",
       "      <td>30</td>\n",
       "      <td>10080</td>\n",
       "      <td>AYDADSGFNGKVLFTISDGNTDSCFNIDMETGQLK</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3654207 rows × 21 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "           ccs_pred  charge  frag_stop_idx  frag_start_idx  miss_cleavage  \\\n",
       "0        315.529022       2             6               0              1   \n",
       "1        304.965790       2            12               6              0   \n",
       "2        304.080536       2            18              12              0   \n",
       "3        305.825348       2            24              18              0   \n",
       "4        330.547638       2            30              24              0   \n",
       "...             ...     ...           ...             ...            ...   \n",
       "3654202  891.748413       4      60404866        60404832              1   \n",
       "3654203  785.478699       3      60404900        60404866              1   \n",
       "3654204  892.459656       4      60404934        60404900              1   \n",
       "3654205  791.322266       4      60404968        60404934              1   \n",
       "3654206  823.819214       4      60405002        60404968              1   \n",
       "\n",
       "         mobility_pred  mod_seq_charge_hash         mod_seq_hash  nAA  \\\n",
       "0             0.775438   471662500970219630   471662500970219628    7   \n",
       "1             0.748912 -5301076820607700088 -5301076820607700090    7   \n",
       "2             0.746970  6057464136741449833  6057464136741449831    7   \n",
       "3             0.751256 -6431722582867031754 -6431722582867031756    7   \n",
       "4             0.814317 -7409729050206298799 -7409729050206298801    7   \n",
       "...                ...                  ...                  ...  ...   \n",
       "3654202       1.108824  7192344052213098708  7192344052213098704   35   \n",
       "3654203       1.302269 -1485306056792248108 -1485306056792248111   35   \n",
       "3654204       1.109729 -1485306056792248107 -1485306056792248111   35   \n",
       "3654205       0.984398  5191231126132273755  5191231126132273751   35   \n",
       "3654206       1.024754 -7707559913944666934 -7707559913944666938   35   \n",
       "\n",
       "         precursor_mz  ...   rt_pred  instrument    irt_pred  is_prot_cterm  \\\n",
       "0          434.249018  ...  0.115377     timsTOF  -37.187631          False   \n",
       "1          414.216952  ...  0.208976     timsTOF  -16.331142          False   \n",
       "2          422.214409  ...  0.158058     timsTOF  -27.677099          False   \n",
       "3          422.214409  ...  0.157143     timsTOF  -27.881022          False   \n",
       "4          513.726727  ...  0.423747     timsTOF   31.526291          False   \n",
       "...               ...  ...       ...         ...         ...            ...   \n",
       "3654202    866.228888  ...  0.831350     timsTOF  122.352159          False   \n",
       "3654203   1159.967730  ...  0.826977     timsTOF  121.377815          False   \n",
       "3654204    870.227616  ...  0.826977     timsTOF  121.377815          False   \n",
       "3654205    976.910866  ...  0.670129     timsTOF   86.427514          False   \n",
       "3654206    958.434460  ...  0.725150     timsTOF   98.687774          False   \n",
       "\n",
       "         is_prot_nterm  mod_sites               mods nce  protein_idxes  \\\n",
       "0                False                                30          19786   \n",
       "1                False                                30           9448   \n",
       "2                False          4        Oxidation@M  30           9448   \n",
       "3                False          2        Oxidation@M  30           9448   \n",
       "4                False          5  Carbamidomethyl@C  30          12819   \n",
       "...                ...        ...                ...  ..            ...   \n",
       "3654202          False                                30            978   \n",
       "3654203          False         17        Oxidation@M  30            978   \n",
       "3654204          False         17        Oxidation@M  30            978   \n",
       "3654205          False                                30           2299   \n",
       "3654206          False         24  Carbamidomethyl@C  30          10080   \n",
       "\n",
       "                                    sequence  \n",
       "0                                    RIHTGQR  \n",
       "1                                    PMPMPVR  \n",
       "2                                    PMPMPVR  \n",
       "3                                    PMPMPVR  \n",
       "4                                    QEWFCTR  \n",
       "...                                      ...  \n",
       "3654202  NLTYVRGSVGPATSTLMFVAGVVGNGLALGILSAR  \n",
       "3654203  NLTYVRGSVGPATSTLMFVAGVVGNGLALGILSAR  \n",
       "3654204  NLTYVRGSVGPATSTLMFVAGVVGNGLALGILSAR  \n",
       "3654205  KNQAADDDDEDLNDTNYDEFNGYAGSLFSSGPYEK  \n",
       "3654206  AYDADSGFNGKVLFTISDGNTDSCFNIDMETGQLK  \n",
       "\n",
       "[3654207 rows x 21 columns]"
      ]
     },
     "execution_count": null,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fasta_lib.precursor_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "python"
    }
   },
   "outputs": [
    {
     "data": {
      "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>description</th>\n",
       "      <th>full_name</th>\n",
       "      <th>gene_name</th>\n",
       "      <th>protein_id</th>\n",
       "      <th>sequence</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>sp|Q9H9K5|MER34_HUMAN Endogenous retroviral en...</td>\n",
       "      <td>sp|Q9H9K5|MER34_HUMAN</td>\n",
       "      <td>ERVMER34-1</td>\n",
       "      <td>Q9H9K5</td>\n",
       "      <td>MGSLSNYALLQLTLTAFLTILVQPQHLLAPVFRTLSILTNQSNCWL...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>sp|P04439|HLAA_HUMAN HLA class I histocompatib...</td>\n",
       "      <td>sp|P04439|HLAA_HUMAN</td>\n",
       "      <td>HLA-A</td>\n",
       "      <td>P04439</td>\n",
       "      <td>MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRF...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>sp|P01911|DRB1_HUMAN HLA class II histocompati...</td>\n",
       "      <td>sp|P01911|DRB1_HUMAN</td>\n",
       "      <td>HLA-DRB1</td>\n",
       "      <td>P01911</td>\n",
       "      <td>MVCLKLPGGSCMTALTVTLMVLSSPLALSGDTRPRFLWQPKRECHF...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>sp|P01889|HLAB_HUMAN HLA class I histocompatib...</td>\n",
       "      <td>sp|P01889|HLAB_HUMAN</td>\n",
       "      <td>HLA-B</td>\n",
       "      <td>P01889</td>\n",
       "      <td>MLVMAPRTVLLLLSAALALTETWAGSHSMRYFYTSVSRPGRGEPRF...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>sp|P31689|DNJA1_HUMAN DnaJ homolog subfamily A...</td>\n",
       "      <td>sp|P31689|DNJA1_HUMAN</td>\n",
       "      <td>DNAJA1</td>\n",
       "      <td>P31689</td>\n",
       "      <td>MVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFK...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20391</th>\n",
       "      <td>sp|Q8WVZ7|RN133_HUMAN E3 ubiquitin-protein lig...</td>\n",
       "      <td>sp|Q8WVZ7|RN133_HUMAN</td>\n",
       "      <td>RNF133</td>\n",
       "      <td>Q8WVZ7</td>\n",
       "      <td>MHLLKVGTWRNNTASSWLMKFSVLWLVSQNCCRASVVWMAYMNISF...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20392</th>\n",
       "      <td>sp|P05387|RLA2_HUMAN 60S acidic ribosomal prot...</td>\n",
       "      <td>sp|P05387|RLA2_HUMAN</td>\n",
       "      <td>RPLP2</td>\n",
       "      <td>P05387</td>\n",
       "      <td>MRYVASYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISEL...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20393</th>\n",
       "      <td>sp|P51991|ROA3_HUMAN Heterogeneous nuclear rib...</td>\n",
       "      <td>sp|P51991|ROA3_HUMAN</td>\n",
       "      <td>HNRNPA3</td>\n",
       "      <td>P51991</td>\n",
       "      <td>MEVKPPPGRPQPDSGRRRRRRGEEGHDPKEPEQLRKLFIGGLSFET...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20394</th>\n",
       "      <td>sp|Q9BZX4|ROP1B_HUMAN Ropporin-1B OS=Homo sapi...</td>\n",
       "      <td>sp|Q9BZX4|ROP1B_HUMAN</td>\n",
       "      <td>ROPN1B</td>\n",
       "      <td>Q9BZX4</td>\n",
       "      <td>MAQTDKPTCIPPELPKMLKEFAKAAIRAQPQDLIQWGADYFEALSR...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20395</th>\n",
       "      <td>sp|P34096|RNAS4_HUMAN Ribonuclease 4 OS=Homo s...</td>\n",
       "      <td>sp|P34096|RNAS4_HUMAN</td>\n",
       "      <td>RNASE4</td>\n",
       "      <td>P34096</td>\n",
       "      <td>MALQRTHSLLLLLLLTLLGLGLVQPSYGQDGMYQRFLRQHVHPEET...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20396 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                             description  \\\n",
       "0      sp|Q9H9K5|MER34_HUMAN Endogenous retroviral en...   \n",
       "1      sp|P04439|HLAA_HUMAN HLA class I histocompatib...   \n",
       "2      sp|P01911|DRB1_HUMAN HLA class II histocompati...   \n",
       "3      sp|P01889|HLAB_HUMAN HLA class I histocompatib...   \n",
       "4      sp|P31689|DNJA1_HUMAN DnaJ homolog subfamily A...   \n",
       "...                                                  ...   \n",
       "20391  sp|Q8WVZ7|RN133_HUMAN E3 ubiquitin-protein lig...   \n",
       "20392  sp|P05387|RLA2_HUMAN 60S acidic ribosomal prot...   \n",
       "20393  sp|P51991|ROA3_HUMAN Heterogeneous nuclear rib...   \n",
       "20394  sp|Q9BZX4|ROP1B_HUMAN Ropporin-1B OS=Homo sapi...   \n",
       "20395  sp|P34096|RNAS4_HUMAN Ribonuclease 4 OS=Homo s...   \n",
       "\n",
       "                   full_name   gene_name protein_id  \\\n",
       "0      sp|Q9H9K5|MER34_HUMAN  ERVMER34-1     Q9H9K5   \n",
       "1       sp|P04439|HLAA_HUMAN       HLA-A     P04439   \n",
       "2       sp|P01911|DRB1_HUMAN    HLA-DRB1     P01911   \n",
       "3       sp|P01889|HLAB_HUMAN       HLA-B     P01889   \n",
       "4      sp|P31689|DNJA1_HUMAN      DNAJA1     P31689   \n",
       "...                      ...         ...        ...   \n",
       "20391  sp|Q8WVZ7|RN133_HUMAN      RNF133     Q8WVZ7   \n",
       "20392   sp|P05387|RLA2_HUMAN       RPLP2     P05387   \n",
       "20393   sp|P51991|ROA3_HUMAN     HNRNPA3     P51991   \n",
       "20394  sp|Q9BZX4|ROP1B_HUMAN      ROPN1B     Q9BZX4   \n",
       "20395  sp|P34096|RNAS4_HUMAN      RNASE4     P34096   \n",
       "\n",
       "                                                sequence  \n",
       "0      MGSLSNYALLQLTLTAFLTILVQPQHLLAPVFRTLSILTNQSNCWL...  \n",
       "1      MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRF...  \n",
       "2      MVCLKLPGGSCMTALTVTLMVLSSPLALSGDTRPRFLWQPKRECHF...  \n",
       "3      MLVMAPRTVLLLLSAALALTETWAGSHSMRYFYTSVSRPGRGEPRF...  \n",
       "4      MVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFK...  \n",
       "...                                                  ...  \n",
       "20391  MHLLKVGTWRNNTASSWLMKFSVLWLVSQNCCRASVVWMAYMNISF...  \n",
       "20392  MRYVASYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISEL...  \n",
       "20393  MEVKPPPGRPQPDSGRRRRRRGEEGHDPKEPEQLRKLFIGGLSFET...  \n",
       "20394  MAQTDKPTCIPPELPKMLKEFAKAAIRAQPQDLIQWGADYFEALSR...  \n",
       "20395  MALQRTHSLLLLLLLTLLGLGLVQPSYGQDGMYQRFLRQHVHPEET...  \n",
       "\n",
       "[20396 rows x 5 columns]"
      ]
     },
     "execution_count": null,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "if 'id' in fasta_lib.protein_df.columns:\n",
    "    fasta_lib.protein_df.rename(columns={'id':'protein_id'}, inplace=True)\n",
    "fasta_lib.protein_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "python"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "3.65M precursors with 241.62M fragments used 6.0145 GB memory\n"
     ]
    }
   ],
   "source": [
    "import os, psutil\n",
    "import numpy as np\n",
    "process = psutil.Process(os.getpid())\n",
    "print(f'{len(fasta_lib.precursor_df)*1e-6:.2f}M precursors with {np.prod(fasta_lib.fragment_mz_df.values.shape, dtype=float)*(1e-6):.2f}M fragments used {process.memory_info().rss/1024**3:.4f} GB memory')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "python"
    }
   },
   "outputs": [],
   "source": [
    "fasta_lib.append_protein_name()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "python"
    }
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 37/37 [1:02:05<00:00, 100.70s/it]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Translation finished, it will take several minutes to export the rest precursors to the tsv file...\n"
     ]
    }
   ],
   "source": [
    "from peptdeep.spec_lib.translate import translate_to_tsv\n",
    "if 'decoy' in fasta_lib.precursor_df.columns:\n",
    "    fasta_lib._precursor_df = fasta_lib.precursor_df[fasta_lib._precursor_df.decoy == 0]\n",
    "translate_to_tsv(\n",
    "    fasta_lib, \n",
    "    output_diann_tsv,\n",
    "    keep_k_highest_fragments=top_k_frag, \n",
    "    min_frag_nAA=min_frag_nAA,\n",
    "    min_frag_mz=min_frag_mz, \n",
    "    min_frag_intensity=frag_inten,\n",
    "    batch_size=100000,\n",
    "    translate_mod_dict=None,\n",
    "    multiprocessing=True,\n",
    ")"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3.8.3 ('base')",
   "language": "python",
   "name": "python3"
  }
 },
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 "nbformat_minor": 2
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