05-label_data.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "\n",
    "from Bio import SeqIO\n",
    "from Bio.SeqRecord import SeqRecord\n",
    "from Bio.Seq import Seq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>class</th>\n",
       "      <th>seqid</th>\n",
       "      <th>seq</th>\n",
       "      <th>set</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>homolog</td>\n",
       "      <td>KEQ67658.1</td>\n",
       "      <td>MLFNSILATAMLFAASAVALPVELEARQSSTTCGNTYYSASQVSAA...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>homolog</td>\n",
       "      <td>XP_013431971.1</td>\n",
       "      <td>MLFKSIFASAVLFAASSIALPTDLEARQQATTCGSTSYSASQVRSA...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>homolog</td>\n",
       "      <td>KEQ81621.1</td>\n",
       "      <td>MLFQSVFTTAVLFVASTIALPTDLESRQSATTCGSTSYTAAQVRSA...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>homolog</td>\n",
       "      <td>XP_013344128.1</td>\n",
       "      <td>MLFQSIFTTAVLFAASAIALPTDLEARQQATRCGSTSYTAAQVRSA...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>homolog</td>\n",
       "      <td>XP_007678837.1</td>\n",
       "      <td>MRFLFATAAFFAAAAFAFPLTQRQSSTTCGKNRYTTKQVNAALNQG...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     class           seqid                                                seq  \\\n",
       "0  homolog      KEQ67658.1  MLFNSILATAMLFAASAVALPVELEARQSSTTCGNTYYSASQVSAA...   \n",
       "1  homolog  XP_013431971.1  MLFKSIFASAVLFAASSIALPTDLEARQQATTCGSTSYSASQVRSA...   \n",
       "2  homolog      KEQ81621.1  MLFQSVFTTAVLFVASTIALPTDLESRQSATTCGSTSYTAAQVRSA...   \n",
       "3  homolog  XP_013344128.1  MLFQSIFTTAVLFAASAIALPTDLEARQQATRCGSTSYTAAQVRSA...   \n",
       "4  homolog  XP_007678837.1  MRFLFATAAFFAAAAFAFPLTQRQSSTTCGKNRYTTKQVNAALNQG...   \n",
       "\n",
       "   set  \n",
       "0  NaN  \n",
       "1  NaN  \n",
       "2  NaN  \n",
       "3  NaN  \n",
       "4  NaN  "
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "eff = pd.read_csv(\"raw/fungal_effectors.tsv\", sep=\"\\t\")\n",
    "\n",
    "eff[\"class\"] = \"effector\"\n",
    "eff.loc[eff[\"Validated\"] == \"no\", \"class\"] = \"homolog\"\n",
    "eff.loc[~eff[\"EffectorP2\"], \"Set\"] = np.nan\n",
    "eff = eff[[\"class\", \"UniqueID\", \"Sequence\", \"Set\"]]\n",
    "eff.rename(columns={\"UniqueID\": \"seqid\", \"Sequence\": \"seq\", \"Set\": \"set\"}, inplace=True)\n",
    "eff.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    }\n",
       "\n",
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       "        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>class</th>\n",
       "      <th>seqid</th>\n",
       "      <th>seq</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>homolog</td>\n",
       "      <td>UniRef90_A0A010PZM0</td>\n",
       "      <td>MKFSTALFTIATLATSVFSTALSPLDNSAVGAVNMDVREVAPLDSS...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>homolog</td>\n",
       "      <td>UniRef90_A0A010Q8R0</td>\n",
       "      <td>MQLSSILLSVGLMAAGADAKLHNAGVCVTNRQEMPVGGTGWSVSYT...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>homolog</td>\n",
       "      <td>UniRef90_A0A010QGI7</td>\n",
       "      <td>MVTFNSLFLAFASVTSVLSAPGELMKRQSTPSSTGTHNGYYYSWWT...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>homolog</td>\n",
       "      <td>UniRef90_A0A010QLX3</td>\n",
       "      <td>MLAKLSLLPLLSAVVSASPLLDARAPVAALDERAVTVSSADLSNFE...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>homolog</td>\n",
       "      <td>UniRef90_A0A010QUB8</td>\n",
       "      <td>MQFSNLVTILSSVAAAAAVSVSYDTGYDDGSRSLTAVSCSDGANGL...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     class                seqid  \\\n",
       "0  homolog  UniRef90_A0A010PZM0   \n",
       "1  homolog  UniRef90_A0A010Q8R0   \n",
       "2  homolog  UniRef90_A0A010QGI7   \n",
       "3  homolog  UniRef90_A0A010QLX3   \n",
       "4  homolog  UniRef90_A0A010QUB8   \n",
       "\n",
       "                                                 seq  \n",
       "0  MKFSTALFTIATLATSVFSTALSPLDNSAVGAVNMDVREVAPLDSS...  \n",
       "1  MQLSSILLSVGLMAAGADAKLHNAGVCVTNRQEMPVGGTGWSVSYT...  \n",
       "2  MVTFNSLFLAFASVTSVLSAPGELMKRQSTPSSTGTHNGYYYSWWT...  \n",
       "3  MLAKLSLLPLLSAVVSASPLLDARAPVAALDERAVTVSSADLSNFE...  \n",
       "4  MQFSNLVTILSSVAAAAAVSVSYDTGYDDGSRSLTAVSCSDGANGL...  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "columns = [\n",
    "    \"target\",\n",
    "    \"query\",\n",
    "    \"evalue\",\n",
    "    \"pident\",\n",
    "    \"bits\",\n",
    "    \"qstart\",\n",
    "    \"qend\",\n",
    "    \"qlen\",\n",
    "    \"tstart\",\n",
    "    \"tend\",\n",
    "    \"tlen\",\n",
    "    \"theader\",\n",
    "    \"sequence\"\n",
    "]\n",
    "\n",
    "eff_hom = pd.read_csv(\n",
    "    \"processed/effector_homologues.tsv\",\n",
    "    sep=\"\\t\",\n",
    "    names=columns,\n",
    "    skipinitialspace=True\n",
    ")\n",
    "\n",
    "eff_hom[\"class\"] = \"homolog\"\n",
    "eff_hom = eff_hom[[\"class\", \"target\", \"sequence\"]]\n",
    "eff_hom.rename(columns={\"target\": \"seqid\", \"sequence\": \"seq\"}, inplace=True)\n",
    "eff_hom.drop_duplicates(inplace=True)\n",
    "\n",
    "eff_hom.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    }\n",
       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>class</th>\n",
       "      <th>seqid</th>\n",
       "      <th>seq</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>secreted</td>\n",
       "      <td>sp|A0A024RXP8|GUX1_HYPJR</td>\n",
       "      <td>MYRKLAVISAFLATARAQSACTLQSETHPPLTWQKCSSGGTCTQQT...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>secreted</td>\n",
       "      <td>sp|A0A024SH20|GUN2_HYPJR</td>\n",
       "      <td>MNKSVAPLLLAASILYGGAAAQQTVWGQCGGIGWSGPTNCAPGSAC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>secreted</td>\n",
       "      <td>sp|A0A024SH76|GUX2_HYPJR</td>\n",
       "      <td>MIVGILTTLATLATLAASVPLEERQACSSVWGQCGGQNWSGPTCCA...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>secreted</td>\n",
       "      <td>sp|A0A024SIB3|XYN3_HYPJR</td>\n",
       "      <td>MKANVILCLLAPLVAALPTETIHLDPELAALRANLTERTADLWDRQ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>secreted</td>\n",
       "      <td>sp|A0A024SNB7|GUN1_HYPJR</td>\n",
       "      <td>MAPSVTLPLTTAILAIARLVAAQQPGTSTPEVHPKLTTYKCTKSGG...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      class                     seqid  \\\n",
       "0  secreted  sp|A0A024RXP8|GUX1_HYPJR   \n",
       "1  secreted  sp|A0A024SH20|GUN2_HYPJR   \n",
       "2  secreted  sp|A0A024SH76|GUX2_HYPJR   \n",
       "3  secreted  sp|A0A024SIB3|XYN3_HYPJR   \n",
       "4  secreted  sp|A0A024SNB7|GUN1_HYPJR   \n",
       "\n",
       "                                                 seq  \n",
       "0  MYRKLAVISAFLATARAQSACTLQSETHPPLTWQKCSSGGTCTQQT...  \n",
       "1  MNKSVAPLLLAASILYGGAAAQQTVWGQCGGIGWSGPTNCAPGSAC...  \n",
       "2  MIVGILTTLATLATLAASVPLEERQACSSVWGQCGGQNWSGPTCCA...  \n",
       "3  MKANVILCLLAPLVAALPTETIHLDPELAALRANLTERTADLWDRQ...  \n",
       "4  MAPSVTLPLTTAILAIARLVAAQQPGTSTPEVHPKLTTYKCTKSGG...  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "localized = pd.read_csv(\"processed/localised.tsv\", sep=\"\\t\", names=[\"class\", \"seqid\", \"seq\"])\n",
    "\n",
    "# There are a small number that appear in the secreted and non-secreted lists.\n",
    "# We'll remove then from the non-secreted.\n",
    "secreted_ids = set(localized.loc[localized[\"class\"] == \"secreted\", \"seqid\"].to_list())\n",
    "\n",
    "localized = localized.loc[\n",
    "    (localized[\"class\"] == \"secreted\") |\n",
    "    ((localized[\"class\"] != \"secreted\") & (~localized[\"seqid\"].isin(secreted_ids)))\n",
    "]\n",
    "\n",
    "localized.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>class</th>\n",
       "      <th>seqid</th>\n",
       "      <th>seq</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>proteome</td>\n",
       "      <td>Bgrahor_DH14_BLGH_07057-mRNA-1</td>\n",
       "      <td>MQDYFHTIVQMEQFYEYTSRNPLHPILVQYRDSPAFQAGSMEEIDS...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>proteome</td>\n",
       "      <td>Bgrahor_DH14_BLGH_07058-mRNA-1</td>\n",
       "      <td>MTPEKRSTTTLMWNVAEQPDYDSTREALQEALKAELTYYTYKSVDK...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>proteome</td>\n",
       "      <td>Bgrahor_DH14_BLGH_07059-mRNA-1</td>\n",
       "      <td>MKISLFASIIAFLSNFMPTLALDGYRCNAQTISREILMREVNKSYD...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>proteome</td>\n",
       "      <td>Bgrahor_DH14_BLGH_06565-mRNA-1</td>\n",
       "      <td>MSLFEELYEYTDQHPLTNLRAEFIQNYDNKIDPMIAIKLLLAKLLI...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>proteome</td>\n",
       "      <td>Bgrahor_DH14_BLGH_06566-mRNA-1</td>\n",
       "      <td>MSLFEELYEYTDQHPLTNLRAEFIQNYDNKIDPMIAIKLLLAKLLI...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      class                           seqid  \\\n",
       "0  proteome  Bgrahor_DH14_BLGH_07057-mRNA-1   \n",
       "1  proteome  Bgrahor_DH14_BLGH_07058-mRNA-1   \n",
       "2  proteome  Bgrahor_DH14_BLGH_07059-mRNA-1   \n",
       "3  proteome  Bgrahor_DH14_BLGH_06565-mRNA-1   \n",
       "4  proteome  Bgrahor_DH14_BLGH_06566-mRNA-1   \n",
       "\n",
       "                                                 seq  \n",
       "0  MQDYFHTIVQMEQFYEYTSRNPLHPILVQYRDSPAFQAGSMEEIDS...  \n",
       "1  MTPEKRSTTTLMWNVAEQPDYDSTREALQEALKAELTYYTYKSVDK...  \n",
       "2  MKISLFASIIAFLSNFMPTLALDGYRCNAQTISREILMREVNKSYD...  \n",
       "3  MSLFEELYEYTDQHPLTNLRAEFIQNYDNKIDPMIAIKLLLAKLLI...  \n",
       "4  MSLFEELYEYTDQHPLTNLRAEFIQNYDNKIDPMIAIKLLLAKLLI...  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "proteomes = pd.read_csv(\"processed/proteomes.tsv\", sep=\"\\t\", names=[\"class\", \"seqid\", \"seq\"])\n",
    "proteomes.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>class</th>\n",
       "      <th>seqid</th>\n",
       "      <th>seq</th>\n",
       "      <th>set</th>\n",
       "      <th>key</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>homolog</td>\n",
       "      <td>KEQ67658.1</td>\n",
       "      <td>MLFNSILATAMLFAASAVALPVELEARQSSTTCGNTYYSASQVSAA...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>KEQ67658.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>homolog</td>\n",
       "      <td>XP_013431971.1</td>\n",
       "      <td>MLFKSIFASAVLFAASSIALPTDLEARQQATTCGSTSYSASQVRSA...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>XP_013431971.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>homolog</td>\n",
       "      <td>KEQ81621.1</td>\n",
       "      <td>MLFQSVFTTAVLFVASTIALPTDLESRQSATTCGSTSYTAAQVRSA...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>KEQ81621.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>homolog</td>\n",
       "      <td>XP_013344128.1</td>\n",
       "      <td>MLFQSIFTTAVLFAASAIALPTDLEARQQATRCGSTSYTAAQVRSA...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>XP_013344128.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>homolog</td>\n",
       "      <td>XP_007678837.1</td>\n",
       "      <td>MRFLFATAAFFAAAAFAFPLTQRQSSTTCGKNRYTTKQVNAALNQG...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>XP_007678837.1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     class           seqid                                                seq  \\\n",
       "0  homolog      KEQ67658.1  MLFNSILATAMLFAASAVALPVELEARQSSTTCGNTYYSASQVSAA...   \n",
       "1  homolog  XP_013431971.1  MLFKSIFASAVLFAASSIALPTDLEARQQATTCGSTSYSASQVRSA...   \n",
       "2  homolog      KEQ81621.1  MLFQSVFTTAVLFVASTIALPTDLESRQSATTCGSTSYTAAQVRSA...   \n",
       "3  homolog  XP_013344128.1  MLFQSIFTTAVLFAASAIALPTDLEARQQATRCGSTSYTAAQVRSA...   \n",
       "4  homolog  XP_007678837.1  MRFLFATAAFFAAAAFAFPLTQRQSSTTCGKNRYTTKQVNAALNQG...   \n",
       "\n",
       "   set             key  \n",
       "0  NaN      KEQ67658.1  \n",
       "1  NaN  XP_013431971.1  \n",
       "2  NaN      KEQ81621.1  \n",
       "3  NaN  XP_013344128.1  \n",
       "4  NaN  XP_007678837.1  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined = pd.concat(\n",
    "    [eff, eff_hom, localized, proteomes],\n",
    "    ignore_index=True\n",
    ")\n",
    "\n",
    "# mmseqs extract swissprot names, which is really annoying.\n",
    "# here we get a special join key just for them.\n",
    "\n",
    "combined[\"key\"] = combined[\"seqid\"]\n",
    "combined.loc[combined[\"key\"].str.startswith('sp|'), \"key\"]\n",
    "\n",
    "combined.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "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>class</th>\n",
       "      <th>seqid</th>\n",
       "      <th>seq</th>\n",
       "      <th>set</th>\n",
       "      <th>key</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>homolog</td>\n",
       "      <td>KEQ67658.1</td>\n",
       "      <td>MLFNSILATAMLFAASAVALPVELEARQSSTTCGNTYYSASQVSAA...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>KEQ67658.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>homolog</td>\n",
       "      <td>XP_013431971.1</td>\n",
       "      <td>MLFKSIFASAVLFAASSIALPTDLEARQQATTCGSTSYSASQVRSA...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>XP_013431971.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>homolog</td>\n",
       "      <td>KEQ81621.1</td>\n",
       "      <td>MLFQSVFTTAVLFVASTIALPTDLESRQSATTCGSTSYTAAQVRSA...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>KEQ81621.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>homolog</td>\n",
       "      <td>XP_013344128.1</td>\n",
       "      <td>MLFQSIFTTAVLFAASAIALPTDLEARQQATRCGSTSYTAAQVRSA...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>XP_013344128.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>homolog</td>\n",
       "      <td>XP_007678837.1</td>\n",
       "      <td>MRFLFATAAFFAAAAFAFPLTQRQSSTTCGKNRYTTKQVNAALNQG...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>XP_007678837.1</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>201881</th>\n",
       "      <td>proteome</td>\n",
       "      <td>Ztri_IPO323_XP_003857810.1</td>\n",
       "      <td>MFTQQLLALTALAAFTSAHSWVEEYQVISDNGSYTGPLGYTRGFVP...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Ztri_IPO323_XP_003857810.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>201882</th>\n",
       "      <td>proteome</td>\n",
       "      <td>Ztri_IPO323_XP_003857811.1</td>\n",
       "      <td>MKPHRIRMAHSLIMNYGLYKKLEIYRAKPASKYEMTQFHTDEYVDF...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Ztri_IPO323_XP_003857811.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>201883</th>\n",
       "      <td>proteome</td>\n",
       "      <td>Ztri_IPO323_XP_003857812.1</td>\n",
       "      <td>MNWYGISVLCLALANVTRAQADPLVDFCRRWSHQTTVVDNKLFIYG...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Ztri_IPO323_XP_003857812.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>201884</th>\n",
       "      <td>proteome</td>\n",
       "      <td>Ztri_IPO323_XP_003857813.1</td>\n",
       "      <td>MSVQQTINEERMENRATLSLQCESRLITSGHTTPDFINRMNSLLQD...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Ztri_IPO323_XP_003857813.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>201885</th>\n",
       "      <td>proteome</td>\n",
       "      <td>Ztri_IPO323_XP_003857814.1</td>\n",
       "      <td>MWPANSPDLNPIKNLWALLKWRLNHNYPLPSSTVVLRQQIQEVWDA...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Ztri_IPO323_XP_003857814.1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>201886 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "           class                       seqid  \\\n",
       "0        homolog                  KEQ67658.1   \n",
       "1        homolog              XP_013431971.1   \n",
       "2        homolog                  KEQ81621.1   \n",
       "3        homolog              XP_013344128.1   \n",
       "4        homolog              XP_007678837.1   \n",
       "...          ...                         ...   \n",
       "201881  proteome  Ztri_IPO323_XP_003857810.1   \n",
       "201882  proteome  Ztri_IPO323_XP_003857811.1   \n",
       "201883  proteome  Ztri_IPO323_XP_003857812.1   \n",
       "201884  proteome  Ztri_IPO323_XP_003857813.1   \n",
       "201885  proteome  Ztri_IPO323_XP_003857814.1   \n",
       "\n",
       "                                                      seq  set  \\\n",
       "0       MLFNSILATAMLFAASAVALPVELEARQSSTTCGNTYYSASQVSAA...  NaN   \n",
       "1       MLFKSIFASAVLFAASSIALPTDLEARQQATTCGSTSYSASQVRSA...  NaN   \n",
       "2       MLFQSVFTTAVLFVASTIALPTDLESRQSATTCGSTSYTAAQVRSA...  NaN   \n",
       "3       MLFQSIFTTAVLFAASAIALPTDLEARQQATRCGSTSYTAAQVRSA...  NaN   \n",
       "4       MRFLFATAAFFAAAAFAFPLTQRQSSTTCGKNRYTTKQVNAALNQG...  NaN   \n",
       "...                                                   ...  ...   \n",
       "201881  MFTQQLLALTALAAFTSAHSWVEEYQVISDNGSYTGPLGYTRGFVP...  NaN   \n",
       "201882  MKPHRIRMAHSLIMNYGLYKKLEIYRAKPASKYEMTQFHTDEYVDF...  NaN   \n",
       "201883  MNWYGISVLCLALANVTRAQADPLVDFCRRWSHQTTVVDNKLFIYG...  NaN   \n",
       "201884  MSVQQTINEERMENRATLSLQCESRLITSGHTTPDFINRMNSLLQD...  NaN   \n",
       "201885  MWPANSPDLNPIKNLWALLKWRLNHNYPLPSSTVVLRQQIQEVWDA...  NaN   \n",
       "\n",
       "                               key  \n",
       "0                       KEQ67658.1  \n",
       "1                   XP_013431971.1  \n",
       "2                       KEQ81621.1  \n",
       "3                   XP_013344128.1  \n",
       "4                   XP_007678837.1  \n",
       "...                            ...  \n",
       "201881  Ztri_IPO323_XP_003857810.1  \n",
       "201882  Ztri_IPO323_XP_003857811.1  \n",
       "201883  Ztri_IPO323_XP_003857812.1  \n",
       "201884  Ztri_IPO323_XP_003857813.1  \n",
       "201885  Ztri_IPO323_XP_003857814.1  \n",
       "\n",
       "[201886 rows x 5 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined.loc[combined[\"key\"].str.startswith('sp|'), \"key\"] = (\n",
    "    combined.loc[combined[\"key\"].str.startswith('sp|'), \"key\"]\n",
    "    .apply(lambda x: x.split('|')[1])\n",
    ")\n",
    "combined"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "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>cluster</th>\n",
       "      <th>member</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Q7Z9I5</td>\n",
       "      <td>Q7Z9I5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Q8SQH8</td>\n",
       "      <td>Q8SQH8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Q8SQH8</td>\n",
       "      <td>Q8SS09</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Q8SQH8</td>\n",
       "      <td>P40994</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Q8SQH8</td>\n",
       "      <td>Pterter_W11_CAA9977015.1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>201886</th>\n",
       "      <td>Q7SDY6</td>\n",
       "      <td>Bgrahor_DH14_BLGH_05980-mRNA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>201887</th>\n",
       "      <td>Q7SDY6</td>\n",
       "      <td>Q6C9T0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>201888</th>\n",
       "      <td>Q7SDY6</td>\n",
       "      <td>Mlin_CH5_jgi|Melli1|196253|MELLI_sc_1023.2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>201889</th>\n",
       "      <td>Q7SDY6</td>\n",
       "      <td>Q9Y7Y2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>201890</th>\n",
       "      <td>Q7SIC2</td>\n",
       "      <td>Q7SIC2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>201891 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       cluster                                      member\n",
       "0       Q7Z9I5                                      Q7Z9I5\n",
       "1       Q8SQH8                                      Q8SQH8\n",
       "2       Q8SQH8                                      Q8SS09\n",
       "3       Q8SQH8                                      P40994\n",
       "4       Q8SQH8                    Pterter_W11_CAA9977015.1\n",
       "...        ...                                         ...\n",
       "201886  Q7SDY6              Bgrahor_DH14_BLGH_05980-mRNA-1\n",
       "201887  Q7SDY6                                      Q6C9T0\n",
       "201888  Q7SDY6  Mlin_CH5_jgi|Melli1|196253|MELLI_sc_1023.2\n",
       "201889  Q7SDY6                                      Q9Y7Y2\n",
       "201890  Q7SIC2                                      Q7SIC2\n",
       "\n",
       "[201891 rows x 2 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "clusters = pd.read_csv(\"processed/clusters.tsv\", sep=\"\\t\", names=[\"cluster\", \"member\"])\n",
    "clusters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "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>cluster</th>\n",
       "      <th>class</th>\n",
       "      <th>seqid</th>\n",
       "      <th>seq</th>\n",
       "      <th>set</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Q7Z9I5</td>\n",
       "      <td>non_secreted</td>\n",
       "      <td>sp|Q7Z9I5|WTF7_SCHPO</td>\n",
       "      <td>MLKMSGSYAPIEDSADELSVHSGNDNEIDLEKGLLPKCNTGNGGTT...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Q8SQH8</td>\n",
       "      <td>non_secreted</td>\n",
       "      <td>sp|Q8SQH8|ARF_ENCCU</td>\n",
       "      <td>MGNMMSKVNNLLYTKLRGLFSGQSERSITMIGLDGAGKTTLLLYLQ...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Q8SQH8</td>\n",
       "      <td>non_secreted</td>\n",
       "      <td>sp|Q8SS09|SAR1_ENCCU</td>\n",
       "      <td>MLDNIQEYLGVVKAKLTEFYEKVFQNFVKSLFGKPSSILFLGIDNA...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Q8SQH8</td>\n",
       "      <td>non_secreted</td>\n",
       "      <td>sp|P40994|ARF3_YEAST</td>\n",
       "      <td>MGNSISKVLGKLFGSKEMKILMLGLDKAGKTTILYKLKLNKIKTST...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Q8SQH8</td>\n",
       "      <td>proteome</td>\n",
       "      <td>Pterter_W11_CAA9977015.1</td>\n",
       "      <td>MLSILRKARLKDKEMRILMLGLDNAGKTTIVKKIMNEDVNSVSPTL...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  cluster         class                     seqid  \\\n",
       "0  Q7Z9I5  non_secreted      sp|Q7Z9I5|WTF7_SCHPO   \n",
       "1  Q8SQH8  non_secreted       sp|Q8SQH8|ARF_ENCCU   \n",
       "2  Q8SQH8  non_secreted      sp|Q8SS09|SAR1_ENCCU   \n",
       "3  Q8SQH8  non_secreted      sp|P40994|ARF3_YEAST   \n",
       "4  Q8SQH8      proteome  Pterter_W11_CAA9977015.1   \n",
       "\n",
       "                                                 seq  set  \n",
       "0  MLKMSGSYAPIEDSADELSVHSGNDNEIDLEKGLLPKCNTGNGGTT...  NaN  \n",
       "1  MGNMMSKVNNLLYTKLRGLFSGQSERSITMIGLDGAGKTTLLLYLQ...  NaN  \n",
       "2  MLDNIQEYLGVVKAKLTEFYEKVFQNFVKSLFGKPSSILFLGIDNA...  NaN  \n",
       "3  MGNSISKVLGKLFGSKEMKILMLGLDKAGKTTILYKLKLNKIKTST...  NaN  \n",
       "4  MLSILRKARLKDKEMRILMLGLDNAGKTTIVKKIMNEDVNSVSPTL...  NaN  "
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_clusters = pd.merge(clusters, combined, left_on=\"member\", right_on=\"key\", how=\"outer\")\n",
    "combined_clusters.drop(columns=[\"member\", \"key\"], inplace=True)\n",
    "\n",
    "# Because we ran the clustering with the localized duplicates, the join will\n",
    "# re-duplicate them.\n",
    "# If you redo this, double check what's actually duplicated before removing things.\n",
    "combined_clusters.drop_duplicates(inplace=True, keep=\"first\")\n",
    "combined_clusters.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "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>cluster</th>\n",
       "      <th>class</th>\n",
       "      <th>seqid</th>\n",
       "      <th>seq</th>\n",
       "      <th>set</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Q7Z9I5</td>\n",
       "      <td>non_secreted</td>\n",
       "      <td>sp|Q7Z9I5|WTF7_SCHPO</td>\n",
       "      <td>MLKMSGSYAPIEDSADELSVHSGNDNEIDLEKGLLPKCNTGNGGTT...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Q8SQH8</td>\n",
       "      <td>non_secreted</td>\n",
       "      <td>sp|Q8SQH8|ARF_ENCCU</td>\n",
       "      <td>MGNMMSKVNNLLYTKLRGLFSGQSERSITMIGLDGAGKTTLLLYLQ...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Q8SQH8</td>\n",
       "      <td>non_secreted</td>\n",
       "      <td>sp|Q8SS09|SAR1_ENCCU</td>\n",
       "      <td>MLDNIQEYLGVVKAKLTEFYEKVFQNFVKSLFGKPSSILFLGIDNA...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Q8SQH8</td>\n",
       "      <td>non_secreted</td>\n",
       "      <td>sp|P40994|ARF3_YEAST</td>\n",
       "      <td>MGNSISKVLGKLFGSKEMKILMLGLDKAGKTTILYKLKLNKIKTST...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Q8SQH8</td>\n",
       "      <td>proteome</td>\n",
       "      <td>Pterter_W11_CAA9977015.1</td>\n",
       "      <td>MLSILRKARLKDKEMRILMLGLDNAGKTTIVKKIMNEDVNSVSPTL...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  cluster         class                     seqid  \\\n",
       "0  Q7Z9I5  non_secreted      sp|Q7Z9I5|WTF7_SCHPO   \n",
       "1  Q8SQH8  non_secreted       sp|Q8SQH8|ARF_ENCCU   \n",
       "2  Q8SQH8  non_secreted      sp|Q8SS09|SAR1_ENCCU   \n",
       "3  Q8SQH8  non_secreted      sp|P40994|ARF3_YEAST   \n",
       "4  Q8SQH8      proteome  Pterter_W11_CAA9977015.1   \n",
       "\n",
       "                                                 seq  set  \n",
       "0  MLKMSGSYAPIEDSADELSVHSGNDNEIDLEKGLLPKCNTGNGGTT...  NaN  \n",
       "1  MGNMMSKVNNLLYTKLRGLFSGQSERSITMIGLDGAGKTTLLLYLQ...  NaN  \n",
       "2  MLDNIQEYLGVVKAKLTEFYEKVFQNFVKSLFGKPSSILFLGIDNA...  NaN  \n",
       "3  MGNSISKVLGKLFGSKEMKILMLGLDKAGKTTILYKLKLNKIKTST...  NaN  \n",
       "4  MLSILRKARLKDKEMRILMLGLDNAGKTTIVKKIMNEDVNSVSPTL...  NaN  "
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_clusters.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "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>cluster</th>\n",
       "      <th>class</th>\n",
       "      <th>seqid</th>\n",
       "      <th>seq</th>\n",
       "      <th>set</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>6042</th>\n",
       "      <td>UniRef90_A0A482LME3</td>\n",
       "      <td>effector</td>\n",
       "      <td>FolSix7</td>\n",
       "      <td>MQVMKYLYLLFHFALFASAIPMLDLFPRQGQCFSTTGSTPPRPPPA...</td>\n",
       "      <td>train</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6130</th>\n",
       "      <td>UniRef90_Q0C912</td>\n",
       "      <td>effector</td>\n",
       "      <td>FGL1</td>\n",
       "      <td>MRLLSLLSVVTLAVASPLSVEEYAKALDERAVSVSTTDFGNFKFYI...</td>\n",
       "      <td>train</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7467</th>\n",
       "      <td>FolSix11</td>\n",
       "      <td>effector</td>\n",
       "      <td>FolSix11</td>\n",
       "      <td>MMFSKAIPISLLISTSHAINICCSSFAGHTCTKDQYNNHRQNVILN...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7475</th>\n",
       "      <td>PST_Pec6</td>\n",
       "      <td>effector</td>\n",
       "      <td>PST_Pec6</td>\n",
       "      <td>MNITYLGTCFLVIATMLGNSDASGASTPKKCKKTIMHEKDKCWTIG...</td>\n",
       "      <td>train</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7478</th>\n",
       "      <td>UmSee1</td>\n",
       "      <td>effector</td>\n",
       "      <td>UmSee1</td>\n",
       "      <td>MLFTTFVSLLLVILCLVHVSAHPLQSFRSSSAIGKQKHKIKSRQFE...</td>\n",
       "      <td>train</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>189890</th>\n",
       "      <td>UniRef90_A0A1B2CW13</td>\n",
       "      <td>effector</td>\n",
       "      <td>MlAvrL2</td>\n",
       "      <td>MGKGNNIQTPCFRASQLRSFCLIAFLLCQSLQSIVSLPALSSKVEL...</td>\n",
       "      <td>train</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>192536</th>\n",
       "      <td>UniRef90_A0A2J8D6X4</td>\n",
       "      <td>effector</td>\n",
       "      <td>VdSCP7</td>\n",
       "      <td>MKTCVIATLVGVAMSAPAMRTSMDAPMMEMANSRPMDMDMGSSTPA...</td>\n",
       "      <td>train</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>197244</th>\n",
       "      <td>UniRef90_A0A139HPX7</td>\n",
       "      <td>effector</td>\n",
       "      <td>CfEcp2</td>\n",
       "      <td>MLFNAAAAAVFAPLLVMGNVLPRNAGNSPGSNRCDASTFNNGQDFD...</td>\n",
       "      <td>train</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>197252</th>\n",
       "      <td>UniRef90_A0A1E1KN96</td>\n",
       "      <td>effector</td>\n",
       "      <td>FolSix3</td>\n",
       "      <td>MRFLLLIAMSMTWVCSIAGLPVEDADSSVGQLQGRGNPYCVFPGRR...</td>\n",
       "      <td>train</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>200701</th>\n",
       "      <td>O74396</td>\n",
       "      <td>effector</td>\n",
       "      <td>PGTG_16791</td>\n",
       "      <td>MSTATIQPTIEDHQQHQTPPLIDLELASPSLAEEQEQEQQEQQEPE...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>178 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    cluster     class       seqid  \\\n",
       "6042    UniRef90_A0A482LME3  effector     FolSix7   \n",
       "6130        UniRef90_Q0C912  effector        FGL1   \n",
       "7467               FolSix11  effector    FolSix11   \n",
       "7475               PST_Pec6  effector    PST_Pec6   \n",
       "7478                 UmSee1  effector      UmSee1   \n",
       "...                     ...       ...         ...   \n",
       "189890  UniRef90_A0A1B2CW13  effector     MlAvrL2   \n",
       "192536  UniRef90_A0A2J8D6X4  effector      VdSCP7   \n",
       "197244  UniRef90_A0A139HPX7  effector      CfEcp2   \n",
       "197252  UniRef90_A0A1E1KN96  effector     FolSix3   \n",
       "200701               O74396  effector  PGTG_16791   \n",
       "\n",
       "                                                      seq    set  \n",
       "6042    MQVMKYLYLLFHFALFASAIPMLDLFPRQGQCFSTTGSTPPRPPPA...  train  \n",
       "6130    MRLLSLLSVVTLAVASPLSVEEYAKALDERAVSVSTTDFGNFKFYI...  train  \n",
       "7467    MMFSKAIPISLLISTSHAINICCSSFAGHTCTKDQYNNHRQNVILN...    NaN  \n",
       "7475    MNITYLGTCFLVIATMLGNSDASGASTPKKCKKTIMHEKDKCWTIG...  train  \n",
       "7478    MLFTTFVSLLLVILCLVHVSAHPLQSFRSSSAIGKQKHKIKSRQFE...  train  \n",
       "...                                                   ...    ...  \n",
       "189890  MGKGNNIQTPCFRASQLRSFCLIAFLLCQSLQSIVSLPALSSKVEL...  train  \n",
       "192536  MKTCVIATLVGVAMSAPAMRTSMDAPMMEMANSRPMDMDMGSSTPA...  train  \n",
       "197244  MLFNAAAAAVFAPLLVMGNVLPRNAGNSPGSNRCDASTFNNGQDFD...  train  \n",
       "197252  MRFLLLIAMSMTWVCSIAGLPVEDADSSVGQLQGRGNPYCVFPGRR...  train  \n",
       "200701  MSTATIQPTIEDHQQHQTPPLIDLELASPSLAEEQEQEQQEQQEPE...    NaN  \n",
       "\n",
       "[178 rows x 5 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_clusters[combined_clusters[\"class\"] == \"effector\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "class_order = {\n",
    "    'effector': 5,\n",
    "    'homolog': 4,\n",
    "    'secreted': 3,\n",
    "    'proteome': 2,\n",
    "    'non_secreted': 1,\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "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>cluster</th>\n",
       "      <th>class</th>\n",
       "      <th>seqid</th>\n",
       "      <th>seq</th>\n",
       "      <th>set</th>\n",
       "      <th>priority</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AKM21218.1</td>\n",
       "      <td>homolog</td>\n",
       "      <td>AKM21218.1</td>\n",
       "      <td>MFFHASEYLLSAILMVSVASSAALPSSQALEPRQGACISALFRPNP...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ALVi.Vi1.11</td>\n",
       "      <td>homolog</td>\n",
       "      <td>ALVi.1389.10</td>\n",
       "      <td>MKPFQFLLISILAASSASAKKHRLCCCAGFDACGLFSCEKDSTQSV...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ALVi.Vi1.11</td>\n",
       "      <td>homolog</td>\n",
       "      <td>ALVi.1389.11</td>\n",
       "      <td>MKLSYPLLVALLAASVSAKKHSLCCCAGFNACNQFVCDDKSTQNIV...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ALVi.Vi1.11</td>\n",
       "      <td>homolog</td>\n",
       "      <td>ALVi.1389.12</td>\n",
       "      <td>MKLLYSLFVSLLAASVSARKHRLCCCAGFNACNQFVCDDYSTQSIV...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ALVi.Vi1.11</td>\n",
       "      <td>homolog</td>\n",
       "      <td>ALVi.1389.13</td>\n",
       "      <td>MMLSYSLLFALLAASVSAKKHRLCCCAGFNACNQFVCDDVHTQNLV...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       cluster    class         seqid  \\\n",
       "0   AKM21218.1  homolog    AKM21218.1   \n",
       "1  ALVi.Vi1.11  homolog  ALVi.1389.10   \n",
       "2  ALVi.Vi1.11  homolog  ALVi.1389.11   \n",
       "3  ALVi.Vi1.11  homolog  ALVi.1389.12   \n",
       "4  ALVi.Vi1.11  homolog  ALVi.1389.13   \n",
       "\n",
       "                                                 seq  set  priority  \n",
       "0  MFFHASEYLLSAILMVSVASSAALPSSQALEPRQGACISALFRPNP...  NaN         4  \n",
       "1  MKPFQFLLISILAASSASAKKHRLCCCAGFDACGLFSCEKDSTQSV...  NaN         4  \n",
       "2  MKLSYPLLVALLAASVSAKKHSLCCCAGFNACNQFVCDDKSTQNIV...  NaN         4  \n",
       "3  MKLLYSLFVSLLAASVSARKHRLCCCAGFNACNQFVCDDYSTQSIV...  NaN         4  \n",
       "4  MMLSYSLLFALLAASVSAKKHRLCCCAGFNACNQFVCDDVHTQNLV...  NaN         4  "
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "def appl(table):\n",
    "    table[\"length\"] = table[\"seq\"].apply(lambda x: len(x))\n",
    "    table.sort_values('length', ascending=False, inplace=True)\n",
    "    \n",
    "    effectors = table.loc[table[\"class\"] == \"effector\"]\n",
    "    secreted = table.loc[table[\"class\"] == \"secreted\"]\n",
    "    non_secreted = table.loc[table[\"class\"] == \"non_secreted\"]\n",
    "\n",
    "    if len(effectors) > 0:\n",
    "        new_cluster = effectors.iloc[0][\"seqid\"]\n",
    "        priority = class_order[\"effector\"]\n",
    "    elif len(secreted) > 0:\n",
    "        new_cluster = secreted.iloc[0][\"seqid\"]\n",
    "        priority = class_order[\"secreted\"]\n",
    "    elif len(non_secreted) > 0:\n",
    "        new_cluster = non_secreted.iloc[0][\"seqid\"]\n",
    "        priority = class_order[\"non_secreted\"]\n",
    "    else:\n",
    "        first_row = table.iloc[0]\n",
    "        new_cluster = first_row[\"cluster\"]\n",
    "        priority = class_order[first_row[\"class\"]]\n",
    "\n",
    "    table[\"new_cluster\"] = new_cluster\n",
    "    table[\"priority\"] = priority\n",
    "    \n",
    "    table.drop(columns=[\"length\"], inplace=True)\n",
    "\n",
    "    sets = set(table[\"set\"].to_list())\n",
    "    if \"test\" in sets:\n",
    "        table[\"set\"] = \"test\"\n",
    "    elif \"train\" in sets:\n",
    "        table[\"set\"] = \"train\"\n",
    "\n",
    "    return table\n",
    "\n",
    "combined_cluster_renamed = combined_clusters.groupby(\"cluster\", as_index=False).apply(appl)\n",
    "combined_cluster_renamed[\"cluster\"] = combined_cluster_renamed[\"new_cluster\"]\n",
    "combined_cluster_renamed.drop(columns=\"new_cluster\", inplace=True)\n",
    "combined_cluster_renamed.sort_values([\"cluster\", \"class\", \"seqid\"], inplace=True, ignore_index=True)\n",
    "combined_cluster_renamed.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "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>cluster</th>\n",
       "      <th>class</th>\n",
       "      <th>seqid</th>\n",
       "      <th>seq</th>\n",
       "      <th>set</th>\n",
       "      <th>priority</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AKM21218.1</td>\n",
       "      <td>homolog</td>\n",
       "      <td>AKM21218.1</td>\n",
       "      <td>MFFHASEYLLSAILMVSVASSAALPSSQALEPRQGACISALFRPNP...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>ALVi.Vi1.11</td>\n",
       "      <td>homolog</td>\n",
       "      <td>ALVi.Vi1.11</td>\n",
       "      <td>MKLFYPLLVYLLTTSVSARRHRLCCCAGFNACNQFVCDDKSTQSII...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>ALVi.Vi1.12</td>\n",
       "      <td>homolog</td>\n",
       "      <td>ALVi.Vi1.12</td>\n",
       "      <td>MKATLISAILLTLSAVDAKKHRLCCCYGIDEDAPGKWSDKSAVCVQ...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>ALVi.Vi1.23</td>\n",
       "      <td>homolog</td>\n",
       "      <td>ALVi.Vi1.23</td>\n",
       "      <td>MKLTFTLLAVSLATSVSANSYTLCCCTKPTNIQDLKDPQYWSGTPP...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>ALVp_11032.1</td>\n",
       "      <td>homolog</td>\n",
       "      <td>ALVp_11032.1</td>\n",
       "      <td>MKLTPALVSSVLISFVSATCYDNCCCTKPQQPSNNWGCDDKAGQAV...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>201861</th>\n",
       "      <td>sp|W7MS18|FUB10_GIBM7</td>\n",
       "      <td>non_secreted</td>\n",
       "      <td>sp|W7MS18|FUB10_GIBM7</td>\n",
       "      <td>MAGDFSNRAPWKRSACDRCRAQKLRCHRDSGHSTDACLRCLKSGIE...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>201863</th>\n",
       "      <td>sp|W7MX26|FUS4_GIBM7</td>\n",
       "      <td>secreted</td>\n",
       "      <td>sp|W7MX26|FUS4_GIBM7</td>\n",
       "      <td>MLTIATLHVALQVFGAFSPSHAAAVTLEHRSARDGNSVAVPANWDV...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>201866</th>\n",
       "      <td>sp|W7N2B2|FUB2_GIBM7</td>\n",
       "      <td>non_secreted</td>\n",
       "      <td>sp|W7N2B2|FUB2_GIBM7</td>\n",
       "      <td>MASELKEYLVIIPDLPDVLAKRQVLLKPHNQDAAPLVKAGRVPFFG...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>201870</th>\n",
       "      <td>sp|W7N2C1|FUB8_GIBM7</td>\n",
       "      <td>non_secreted</td>\n",
       "      <td>sp|W7N2C1|FUB8_GIBM7</td>\n",
       "      <td>MQKIAKQALSSLSSLAKSPANAMGSISHLPAYGHRLLPVLIDEISR...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>201885</th>\n",
       "      <td>sp|W8QRE4|XYL5_PHACH</td>\n",
       "      <td>secreted</td>\n",
       "      <td>sp|W8QRE4|XYL5_PHACH</td>\n",
       "      <td>MAYLKVSGTKIVDKDGNEVILRGAGLGGWMNMENFITGYPGCEFQI...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>76662 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                      cluster         class                  seqid  \\\n",
       "0                  AKM21218.1       homolog             AKM21218.1   \n",
       "10                ALVi.Vi1.11       homolog            ALVi.Vi1.11   \n",
       "19                ALVi.Vi1.12       homolog            ALVi.Vi1.12   \n",
       "20                ALVi.Vi1.23       homolog            ALVi.Vi1.23   \n",
       "42               ALVp_11032.1       homolog           ALVp_11032.1   \n",
       "...                       ...           ...                    ...   \n",
       "201861  sp|W7MS18|FUB10_GIBM7  non_secreted  sp|W7MS18|FUB10_GIBM7   \n",
       "201863   sp|W7MX26|FUS4_GIBM7      secreted   sp|W7MX26|FUS4_GIBM7   \n",
       "201866   sp|W7N2B2|FUB2_GIBM7  non_secreted   sp|W7N2B2|FUB2_GIBM7   \n",
       "201870   sp|W7N2C1|FUB8_GIBM7  non_secreted   sp|W7N2C1|FUB8_GIBM7   \n",
       "201885   sp|W8QRE4|XYL5_PHACH      secreted   sp|W8QRE4|XYL5_PHACH   \n",
       "\n",
       "                                                      seq  set  priority  \n",
       "0       MFFHASEYLLSAILMVSVASSAALPSSQALEPRQGACISALFRPNP...  NaN         4  \n",
       "10      MKLFYPLLVYLLTTSVSARRHRLCCCAGFNACNQFVCDDKSTQSII...  NaN         4  \n",
       "19      MKATLISAILLTLSAVDAKKHRLCCCYGIDEDAPGKWSDKSAVCVQ...  NaN         4  \n",
       "20      MKLTFTLLAVSLATSVSANSYTLCCCTKPTNIQDLKDPQYWSGTPP...  NaN         4  \n",
       "42      MKLTPALVSSVLISFVSATCYDNCCCTKPQQPSNNWGCDDKAGQAV...  NaN         4  \n",
       "...                                                   ...  ...       ...  \n",
       "201861  MAGDFSNRAPWKRSACDRCRAQKLRCHRDSGHSTDACLRCLKSGIE...  NaN         1  \n",
       "201863  MLTIATLHVALQVFGAFSPSHAAAVTLEHRSARDGNSVAVPANWDV...  NaN         3  \n",
       "201866  MASELKEYLVIIPDLPDVLAKRQVLLKPHNQDAAPLVKAGRVPFFG...  NaN         1  \n",
       "201870  MQKIAKQALSSLSSLAKSPANAMGSISHLPAYGHRLLPVLIDEISR...  NaN         1  \n",
       "201885  MAYLKVSGTKIVDKDGNEVILRGAGLGGWMNMENFITGYPGCEFQI...  NaN         3  \n",
       "\n",
       "[76662 rows x 6 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_cluster_renamed.loc[combined_cluster_renamed[\"cluster\"] == combined_cluster_renamed[\"seqid\"]]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "rep = (\n",
    "    combined_cluster_renamed\n",
    "    .loc[combined_cluster_renamed[\"cluster\"] == combined_cluster_renamed[\"seqid\"]]\n",
    "    .sort_values([\"cluster\", \"priority\"], ascending=False)\n",
    "    .groupby(\"cluster\")\n",
    "    .first()\n",
    "    .sort_values(\"priority\", ascending=False)\n",
    "    .reset_index()\n",
    ")\n",
    "\n",
    "def map_fun(df, test_proportion=0.2):\n",
    "    samples = df[df[\"set\"].isnull()].sample(frac=test_proportion).index\n",
    "    df.loc[samples, \"set\"] = \"test\"\n",
    "    return df.fillna(value=\"train\")\n",
    "\n",
    "rep = (\n",
    "    rep\n",
    "    .groupby(\"class\", as_index=False)\n",
    "    .apply(map_fun)\n",
    "    [[\"cluster\", \"set\"]]\n",
    "    .set_index(\"cluster\", drop=True)\n",
    "    [\"set\"]\n",
    "    .to_dict()\n",
    ")\n",
    "#rep"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_cluster_renamed[\"set\"] = combined_cluster_renamed[\"cluster\"].apply(lambda x: rep[x])\n",
    "combined_cluster_renamed.to_csv(\"processed/representative.tsv\", sep=\"\\t\", index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "76662"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "representatives = combined_cluster_renamed.loc[\n",
    "    (combined_cluster_renamed[\"cluster\"] == combined_cluster_renamed[\"seqid\"]),\n",
    "    [\"cluster\", \"seq\"]\n",
    "]\n",
    "\n",
    "representative_seqs = []\n",
    "\n",
    "for i, row in representatives.iterrows():\n",
    "    seq = Seq(row[\"seq\"])\n",
    "    sr = SeqRecord(seq, id=row[\"cluster\"], name=row[\"cluster\"], description=row[\"cluster\"])\n",
    "    representative_seqs.append(sr)\n",
    "\n",
    "SeqIO.write(representative_seqs, \"processed/representative.fasta\", \"fasta\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "15330"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "test = combined_cluster_renamed.loc[\n",
    "    ((combined_cluster_renamed[\"cluster\"] == combined_cluster_renamed[\"seqid\"]) &\n",
    "     (combined_cluster_renamed[\"set\"] == \"test\")),\n",
    "    [\"cluster\", \"seq\"]\n",
    "]\n",
    "\n",
    "test_seqs = []\n",
    "\n",
    "for i, row in test.iterrows():\n",
    "    seq = Seq(row[\"seq\"])\n",
    "    sr = SeqRecord(seq, id=row[\"cluster\"], name=row[\"cluster\"], description=row[\"cluster\"])\n",
    "    test_seqs.append(sr)\n",
    "\n",
    "SeqIO.write(test_seqs, \"processed/test.fasta\", \"fasta\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "61332"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "train = combined_cluster_renamed.loc[\n",
    "    ((combined_cluster_renamed[\"cluster\"] == combined_cluster_renamed[\"seqid\"]) &\n",
    "     (combined_cluster_renamed[\"set\"] == \"train\")),\n",
    "    [\"cluster\", \"seq\"]\n",
    "]\n",
    "\n",
    "train_seqs = []\n",
    "\n",
    "for i, row in train.iterrows():\n",
    "    seq = Seq(row[\"seq\"])\n",
    "    sr = SeqRecord(seq, id=row[\"cluster\"], name=row[\"cluster\"], description=row[\"cluster\"])\n",
    "    train_seqs.append(sr)\n",
    "\n",
    "SeqIO.write(train_seqs, \"processed/train.fasta\", \"fasta\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<function setattr(obj, name, value, /)>"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "setattr"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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