Guaymas_parse.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import subprocess\n",
    "import sys\n",
    "sys.path.append(\"..\")\n",
    "from src.useful import *"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Parse HMM Search Output"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "columns = ['target_name', 'target_accession', 'query_name', 'query_accession', 'full_sequence_evalue', 'full_sequence_score', 'full_sequence_bias', 'domain_e_evalue', 'domain_score', 'domain_bias', 'domain#est_exp', 'domain#est_reg', 'domain#est_clu', 'domain#est_ov', 'domain#est_env', 'domain#est_dom', 'domain#est_rep', 'domain#est_inc', 'description_of_target']\n",
    "root_path = '../../data/results/hmmer_searches/'\n",
    "all_bins_hmmer_fp = root_path + 'PET_search.hmmsearch_out'\n",
    "\n",
    "sep='\\s+'\n",
    "df = pd.read_csv(all_bins_hmmer_fp, sep=sep, skiprows=3, skipfooter=10, header=None, names=columns, index_col=False, engine='python')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Make a dive_core_horizon column to eventually add on temperature data for each dive \n",
    "df['dive'] = df['target_name'].str.split('_').str[0:3].str.join('_')\n",
    "\n",
    "#Read in fasta file and add columns for protein sequence and protein sequence length\n",
    "guaymas2020_bins_fp = 'Guaymas2020bins_all.faa'\n",
    "guaymas2020_bins_df = fasta2df(guaymas2020_bins_fp)\n",
    "guaymas2020_bins_df['aa_sequence_length'] = guaymas2020_bins_df['aa_sequence'].str.len()\n",
    "\n",
    "#Join aa_sequence and aa_sequence column to df from guaymas2020_bins_df using target_name as key\n",
    "df = df.merge(guaymas2020_bins_df, left_on='target_name', right_on='ProteinID', how='left')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "df['dive'].unique()\n",
    "#Build dictionary that connects each dive to its corresponding temperature\n",
    "dive_temps = {'D4993_C5_LG':'35' , 'D4993_C5_H2': '72', 'D4993_C5_H1':'29', 'D4993_C5_H3':'33',\n",
    "       'D4994_C39_H1':'89', 'D4994_C39_H2':'99', 'D4998_C1112_H1':'80', 'D4998_C2223_H2':'15',\n",
    "       'D4998_C1112_H2':'100', 'D4991_C11_H1':'10', 'D4993_C5_H4': '39', 'D4998_C2223_H1':'4',\n",
    "       'D4998_C1112_H3':'115'}\n",
    "\n",
    "#Add temperature column to df\n",
    "df['temperature'] = df['dive'].map(dive_temps)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Write out fasta files for each protein\n",
    "pet_fp = '../../data/results/PETHits_Guaymas2020_ALLBINS.fasta'\n",
    "with open(pet_fp, 'w') as f:\n",
    "    for seq in df[['target_name', 'aa_sequence']].values:\n",
    "        f.write('>' + seq[0] + '\\n')\n",
    "        f.write(seq[1] + '\\n')\n",
    "    f.close()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Sort by e-value, temperature and de-duplicate hits"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Rearrange so that the lowest e-value is at the top\n",
    "pet_new = df.sort_values(by=['full_sequence_evalue'], ascending=True)\n",
    "\n",
    "#Find duplicates that have the same aa_sequence and keep the one with the highest temperature\n",
    "pet_new = pet_new.sort_values(by=['temperature'], ascending=False)\n",
    "pet_new = pet_new.drop_duplicates(subset=['aa_sequence'], keep='first')\n",
    "#pet_new.head(200).tail(50)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Write deduplicated pet_new to fasta files to save for later use\n",
    "pet_fp = '../../data/results/PETHits_deduplicated_Guaymas2020_ALLBINS.fasta'\n",
    "with open(pet_fp, 'w') as f:\n",
    "    for seq in pet_new[['target_name', 'aa_sequence']].values:\n",
    "        f.write('>' + seq[0] + '\\n')\n",
    "        f.write(seq[1] + '\\n')\n",
    "    f.close()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Add on Phylogeny metadata "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Add phylogenetic annotation to pet_new\n",
    "#Read in phylogenetic annotations\n",
    "arc_fp = 'gtdbtk.ar53.summary.tsv'\n",
    "bac_fp = 'gtdbtk.bac120.summary.tsv'\n",
    "arc_df = pd.read_csv(arc_fp, sep='\\t')\n",
    "bac_df = pd.read_csv(bac_fp, sep='\\t')\n",
    "arc_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "arc = arc_df[['user_genome', 'classification']]\n",
    "bac = bac_df[['user_genome', 'classification']]\n",
    "#arc['Domain'] = arc['classification'].str.split(';').str[0].str.split('__').str[1]\n",
    "#bac['Domain'] = bac['classification'].str.split(';').str[0].str.split('__').str[1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Split classification by ; and pivot so that each level of classification is a column\n",
    "arc = arc.join(arc['classification'].str.split(';', expand=True).add_prefix('level_'))\n",
    "bac = bac.join(bac['classification'].str.split(';', expand=True).add_prefix('level_'))\n",
    "#arc.drop(columns=['classification'], inplace=True)\n",
    "#bac.drop(columns=['classification'], inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Split the target name to retrieve the bin and create a new column with bin name  \n",
    "pet_new['Bin'] = pet_new['target_name'].str.split('_').str[0:5].str.join('_')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>user_genome</th>\n",
       "      <th>classification</th>\n",
       "      <th>level_0</th>\n",
       "      <th>level_1</th>\n",
       "      <th>level_2</th>\n",
       "      <th>level_3</th>\n",
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       "      <th>level_5</th>\n",
       "      <th>level_6</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>D4991_C11_H1_Bin_10</td>\n",
       "      <td>d__Archaea;p__Halobacteriota;c__Syntropharchae...</td>\n",
       "      <td>d__Archaea</td>\n",
       "      <td>p__Halobacteriota</td>\n",
       "      <td>c__Syntropharchaeia</td>\n",
       "      <td>o__Syntropharchaeales</td>\n",
       "      <td>f__Syntropharchaeaceae</td>\n",
       "      <td>g__Syntropharchaeum_A</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>D4991_C11_H1_Bin_108</td>\n",
       "      <td>d__Archaea;p__Thermoplasmatota;c__E2;o__DHVEG-...</td>\n",
       "      <td>d__Archaea</td>\n",
       "      <td>p__Thermoplasmatota</td>\n",
       "      <td>c__E2</td>\n",
       "      <td>o__DHVEG-1</td>\n",
       "      <td>f__B8-G13</td>\n",
       "      <td>g__B8-G13</td>\n",
       "      <td>s__B8-G13 sp021162485</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>D4991_C11_H1_Bin_113</td>\n",
       "      <td>d__Archaea;p__Iainarchaeota;c__Iainarchaeia;o_...</td>\n",
       "      <td>d__Archaea</td>\n",
       "      <td>p__Iainarchaeota</td>\n",
       "      <td>c__Iainarchaeia</td>\n",
       "      <td>o__Iainarchaeales</td>\n",
       "      <td>f__JAFCCW01</td>\n",
       "      <td>g__JAFCCW01</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>D4991_C11_H1_Bin_119</td>\n",
       "      <td>d__Archaea;p__Altiarchaeota;c__Altiarchaeia;o_...</td>\n",
       "      <td>d__Archaea</td>\n",
       "      <td>p__Altiarchaeota</td>\n",
       "      <td>c__Altiarchaeia</td>\n",
       "      <td>o__IMC4</td>\n",
       "      <td>f__</td>\n",
       "      <td>g__</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>D4991_C11_H1_Bin_12</td>\n",
       "      <td>d__Archaea;p__Thermoproteota;c__Bathyarchaeia;...</td>\n",
       "      <td>d__Archaea</td>\n",
       "      <td>p__Thermoproteota</td>\n",
       "      <td>c__Bathyarchaeia</td>\n",
       "      <td>o__B26-1</td>\n",
       "      <td>f__UBA233</td>\n",
       "      <td>g__PIYA01</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "            user_genome                                     classification  \\\n",
       "0   D4991_C11_H1_Bin_10  d__Archaea;p__Halobacteriota;c__Syntropharchae...   \n",
       "1  D4991_C11_H1_Bin_108  d__Archaea;p__Thermoplasmatota;c__E2;o__DHVEG-...   \n",
       "2  D4991_C11_H1_Bin_113  d__Archaea;p__Iainarchaeota;c__Iainarchaeia;o_...   \n",
       "3  D4991_C11_H1_Bin_119  d__Archaea;p__Altiarchaeota;c__Altiarchaeia;o_...   \n",
       "4   D4991_C11_H1_Bin_12  d__Archaea;p__Thermoproteota;c__Bathyarchaeia;...   \n",
       "\n",
       "      level_0              level_1              level_2  \\\n",
       "0  d__Archaea    p__Halobacteriota  c__Syntropharchaeia   \n",
       "1  d__Archaea  p__Thermoplasmatota                c__E2   \n",
       "2  d__Archaea     p__Iainarchaeota      c__Iainarchaeia   \n",
       "3  d__Archaea     p__Altiarchaeota      c__Altiarchaeia   \n",
       "4  d__Archaea    p__Thermoproteota     c__Bathyarchaeia   \n",
       "\n",
       "                 level_3                 level_4                level_5  \\\n",
       "0  o__Syntropharchaeales  f__Syntropharchaeaceae  g__Syntropharchaeum_A   \n",
       "1             o__DHVEG-1               f__B8-G13              g__B8-G13   \n",
       "2      o__Iainarchaeales             f__JAFCCW01            g__JAFCCW01   \n",
       "3                o__IMC4                     f__                    g__   \n",
       "4               o__B26-1               f__UBA233              g__PIYA01   \n",
       "\n",
       "                 level_6  \n",
       "0                    s__  \n",
       "1  s__B8-G13 sp021162485  \n",
       "2                    s__  \n",
       "3                    s__  \n",
       "4                    s__  "
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Concatenate the arc and bac dataframes\n",
    "phylo = pd.concat([arc, bac])\n",
    "phylo.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>target_name</th>\n",
       "      <th>query_name</th>\n",
       "      <th>full_sequence_evalue</th>\n",
       "      <th>full_sequence_score</th>\n",
       "      <th>full_sequence_bias</th>\n",
       "      <th>domain_e_evalue</th>\n",
       "      <th>domain_score</th>\n",
       "      <th>domain_bias</th>\n",
       "      <th>dive</th>\n",
       "      <th>ProteinID</th>\n",
       "      <th>...</th>\n",
       "      <th>Bin</th>\n",
       "      <th>user_genome</th>\n",
       "      <th>classification</th>\n",
       "      <th>level_0</th>\n",
       "      <th>level_1</th>\n",
       "      <th>level_2</th>\n",
       "      <th>level_3</th>\n",
       "      <th>level_4</th>\n",
       "      <th>level_5</th>\n",
       "      <th>level_6</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>D4998_C1112_H3_Bin_13_scaffold_290638_2</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>1.900000e-08</td>\n",
       "      <td>43.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.300000e-08</td>\n",
       "      <td>42.3</td>\n",
       "      <td>0.0</td>\n",
       "      <td>D4998_C1112_H3</td>\n",
       "      <td>D4998_C1112_H3_Bin_13_scaffold_290638_2</td>\n",
       "      <td>...</td>\n",
       "      <td>D4998_C1112_H3_Bin_13</td>\n",
       "      <td>D4998_C1112_H3_Bin_13</td>\n",
       "      <td>d__Bacteria;p__Planctomycetota;c__Planctomycet...</td>\n",
       "      <td>d__Bacteria</td>\n",
       "      <td>p__Planctomycetota</td>\n",
       "      <td>c__Planctomycetia</td>\n",
       "      <td>o__Pirellulales</td>\n",
       "      <td>f__Pirellulaceae</td>\n",
       "      <td>g__UWMA-0346</td>\n",
       "      <td>s__UWMA-0346 sp012959465</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>D4998_C1112_H3_Bin_22_scaffold_55156_3</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>1.500000e-08</td>\n",
       "      <td>43.4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>8.600000e-02</td>\n",
       "      <td>21.2</td>\n",
       "      <td>0.0</td>\n",
       "      <td>D4998_C1112_H3</td>\n",
       "      <td>D4998_C1112_H3_Bin_22_scaffold_55156_3</td>\n",
       "      <td>...</td>\n",
       "      <td>D4998_C1112_H3_Bin_22</td>\n",
       "      <td>D4998_C1112_H3_Bin_22</td>\n",
       "      <td>d__Archaea;p__Thermoproteota;c__Thermoprotei;o...</td>\n",
       "      <td>d__Archaea</td>\n",
       "      <td>p__Thermoproteota</td>\n",
       "      <td>c__Thermoprotei</td>\n",
       "      <td>o__Thermofilales</td>\n",
       "      <td>f__</td>\n",
       "      <td>g__</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>D4998_C1112_H3_Bin_150_scaffold_19950_40</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>3.400000e-06</td>\n",
       "      <td>35.7</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.500000e-02</td>\n",
       "      <td>23.7</td>\n",
       "      <td>0.0</td>\n",
       "      <td>D4998_C1112_H3</td>\n",
       "      <td>D4998_C1112_H3_Bin_150_scaffold_19950_40</td>\n",
       "      <td>...</td>\n",
       "      <td>D4998_C1112_H3_Bin_150</td>\n",
       "      <td>D4998_C1112_H3_Bin_150</td>\n",
       "      <td>d__Archaea;p__Thermoproteota;c__Thermoprotei_A...</td>\n",
       "      <td>d__Archaea</td>\n",
       "      <td>p__Thermoproteota</td>\n",
       "      <td>c__Thermoprotei_A</td>\n",
       "      <td>o__Sulfolobales</td>\n",
       "      <td>f__Desulfurococcaceae</td>\n",
       "      <td>g__JAGGXK01</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>D4998_C1112_H3_Bin_41_scaffold_101953_3</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>2.200000e-08</td>\n",
       "      <td>42.8</td>\n",
       "      <td>1.8</td>\n",
       "      <td>3.200000e-08</td>\n",
       "      <td>42.3</td>\n",
       "      <td>1.8</td>\n",
       "      <td>D4998_C1112_H3</td>\n",
       "      <td>D4998_C1112_H3_Bin_41_scaffold_101953_3</td>\n",
       "      <td>...</td>\n",
       "      <td>D4998_C1112_H3_Bin_41</td>\n",
       "      <td>D4998_C1112_H3_Bin_41</td>\n",
       "      <td>d__Bacteria;p__Planctomycetota;c__UBA1135;o__U...</td>\n",
       "      <td>d__Bacteria</td>\n",
       "      <td>p__Planctomycetota</td>\n",
       "      <td>c__UBA1135</td>\n",
       "      <td>o__UBA1135</td>\n",
       "      <td>f__GCA-002686595</td>\n",
       "      <td>g__DUCM01</td>\n",
       "      <td>s__DUCM01 sp012959785</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>D4998_C1112_H3_Bin_198_scaffold_234535_28</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>1.800000e-08</td>\n",
       "      <td>43.2</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.200000e-02</td>\n",
       "      <td>24.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>D4998_C1112_H3</td>\n",
       "      <td>D4998_C1112_H3_Bin_198_scaffold_234535_28</td>\n",
       "      <td>...</td>\n",
       "      <td>D4998_C1112_H3_Bin_198</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 23 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                 target_name  \\\n",
       "0    D4998_C1112_H3_Bin_13_scaffold_290638_2   \n",
       "1     D4998_C1112_H3_Bin_22_scaffold_55156_3   \n",
       "2   D4998_C1112_H3_Bin_150_scaffold_19950_40   \n",
       "3    D4998_C1112_H3_Bin_41_scaffold_101953_3   \n",
       "4  D4998_C1112_H3_Bin_198_scaffold_234535_28   \n",
       "\n",
       "                                     query_name  full_sequence_evalue  \\\n",
       "0  00129_Cutinase_Thermobifida_fusca_PET_muscle          1.900000e-08   \n",
       "1  00129_Cutinase_Thermobifida_fusca_PET_muscle          1.500000e-08   \n",
       "2  00129_Cutinase_Thermobifida_fusca_PET_muscle          3.400000e-06   \n",
       "3  00129_Cutinase_Thermobifida_fusca_PET_muscle          2.200000e-08   \n",
       "4  00129_Cutinase_Thermobifida_fusca_PET_muscle          1.800000e-08   \n",
       "\n",
       "   full_sequence_score  full_sequence_bias  domain_e_evalue  domain_score  \\\n",
       "0                 43.0                 0.0     3.300000e-08          42.3   \n",
       "1                 43.4                 0.0     8.600000e-02          21.2   \n",
       "2                 35.7                 0.0     1.500000e-02          23.7   \n",
       "3                 42.8                 1.8     3.200000e-08          42.3   \n",
       "4                 43.2                 0.0     1.200000e-02          24.0   \n",
       "\n",
       "   domain_bias            dive                                  ProteinID  \\\n",
       "0          0.0  D4998_C1112_H3    D4998_C1112_H3_Bin_13_scaffold_290638_2   \n",
       "1          0.0  D4998_C1112_H3     D4998_C1112_H3_Bin_22_scaffold_55156_3   \n",
       "2          0.0  D4998_C1112_H3   D4998_C1112_H3_Bin_150_scaffold_19950_40   \n",
       "3          1.8  D4998_C1112_H3    D4998_C1112_H3_Bin_41_scaffold_101953_3   \n",
       "4          0.0  D4998_C1112_H3  D4998_C1112_H3_Bin_198_scaffold_234535_28   \n",
       "\n",
       "   ...                     Bin             user_genome  \\\n",
       "0  ...   D4998_C1112_H3_Bin_13   D4998_C1112_H3_Bin_13   \n",
       "1  ...   D4998_C1112_H3_Bin_22   D4998_C1112_H3_Bin_22   \n",
       "2  ...  D4998_C1112_H3_Bin_150  D4998_C1112_H3_Bin_150   \n",
       "3  ...   D4998_C1112_H3_Bin_41   D4998_C1112_H3_Bin_41   \n",
       "4  ...  D4998_C1112_H3_Bin_198                     NaN   \n",
       "\n",
       "                                      classification      level_0  \\\n",
       "0  d__Bacteria;p__Planctomycetota;c__Planctomycet...  d__Bacteria   \n",
       "1  d__Archaea;p__Thermoproteota;c__Thermoprotei;o...   d__Archaea   \n",
       "2  d__Archaea;p__Thermoproteota;c__Thermoprotei_A...   d__Archaea   \n",
       "3  d__Bacteria;p__Planctomycetota;c__UBA1135;o__U...  d__Bacteria   \n",
       "4                                                NaN          NaN   \n",
       "\n",
       "              level_1            level_2           level_3  \\\n",
       "0  p__Planctomycetota  c__Planctomycetia   o__Pirellulales   \n",
       "1   p__Thermoproteota    c__Thermoprotei  o__Thermofilales   \n",
       "2   p__Thermoproteota  c__Thermoprotei_A   o__Sulfolobales   \n",
       "3  p__Planctomycetota         c__UBA1135        o__UBA1135   \n",
       "4                 NaN                NaN               NaN   \n",
       "\n",
       "                 level_4       level_5                   level_6  \n",
       "0       f__Pirellulaceae  g__UWMA-0346  s__UWMA-0346 sp012959465  \n",
       "1                    f__           g__                       s__  \n",
       "2  f__Desulfurococcaceae   g__JAGGXK01                       s__  \n",
       "3       f__GCA-002686595     g__DUCM01     s__DUCM01 sp012959785  \n",
       "4                    NaN           NaN                       NaN  \n",
       "\n",
       "[5 rows x 23 columns]"
      ]
     },
     "execution_count": 45,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Join arc and bac to pet_new\n",
    "pet_new = pet_new.merge(phylo, left_on='Bin', right_on='user_genome', how='left')\n",
    "pet_new.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(363, 23)"
      ]
     },
     "execution_count": 46,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Sort on lowest e-value and highest temperature and then choose the top unique columns by classification\n",
    "pet_new = pet_new.sort_values(by=['full_sequence_evalue', 'temperature'], ascending=[True, False])\n",
    "pet_new_ = pet_new.drop_duplicates(subset=['classification'], keep='first')\n",
    "pet_new.shape "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(196, 23)"
      ]
     },
     "execution_count": 47,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pet_new_.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "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>target_name</th>\n",
       "      <th>query_name</th>\n",
       "      <th>full_sequence_evalue</th>\n",
       "      <th>full_sequence_score</th>\n",
       "      <th>full_sequence_bias</th>\n",
       "      <th>domain_e_evalue</th>\n",
       "      <th>domain_score</th>\n",
       "      <th>domain_bias</th>\n",
       "      <th>dive</th>\n",
       "      <th>ProteinID</th>\n",
       "      <th>...</th>\n",
       "      <th>Bin</th>\n",
       "      <th>user_genome</th>\n",
       "      <th>classification</th>\n",
       "      <th>level_0</th>\n",
       "      <th>level_1</th>\n",
       "      <th>level_2</th>\n",
       "      <th>level_3</th>\n",
       "      <th>level_4</th>\n",
       "      <th>level_5</th>\n",
       "      <th>level_6</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>272</th>\n",
       "      <td>D4993_C5_H1_Bin_524_scaffold_590470_15</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>1.600000e-42</td>\n",
       "      <td>154.8</td>\n",
       "      <td>7.8</td>\n",
       "      <td>3.500000e-12</td>\n",
       "      <td>55.3</td>\n",
       "      <td>0.3</td>\n",
       "      <td>D4993_C5_H1</td>\n",
       "      <td>D4993_C5_H1_Bin_524_scaffold_590470_15</td>\n",
       "      <td>...</td>\n",
       "      <td>D4993_C5_H1_Bin_524</td>\n",
       "      <td>D4993_C5_H1_Bin_524</td>\n",
       "      <td>d__Bacteria;p__Chloroflexota;c__Anaerolineae;o...</td>\n",
       "      <td>d__Bacteria</td>\n",
       "      <td>p__Chloroflexota</td>\n",
       "      <td>c__Anaerolineae</td>\n",
       "      <td>o__JAFGEY01</td>\n",
       "      <td>f__JAFGEY01</td>\n",
       "      <td>g__</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>158</th>\n",
       "      <td>D4993_C5_H4_Bin_238_scaffold_20386_9</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>2.100000e-20</td>\n",
       "      <td>82.3</td>\n",
       "      <td>0.1</td>\n",
       "      <td>2.900000e-20</td>\n",
       "      <td>81.8</td>\n",
       "      <td>0.1</td>\n",
       "      <td>D4993_C5_H4</td>\n",
       "      <td>D4993_C5_H4_Bin_238_scaffold_20386_9</td>\n",
       "      <td>...</td>\n",
       "      <td>D4993_C5_H4_Bin_238</td>\n",
       "      <td>D4993_C5_H4_Bin_238</td>\n",
       "      <td>d__Archaea;p__Thermoproteota;c__Bathyarchaeia;...</td>\n",
       "      <td>d__Archaea</td>\n",
       "      <td>p__Thermoproteota</td>\n",
       "      <td>c__Bathyarchaeia</td>\n",
       "      <td>o__B26-1</td>\n",
       "      <td>f__WUQV01</td>\n",
       "      <td>g__</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>332</th>\n",
       "      <td>D4998_C2223_H2_Bin_329_scaffold_361784_9</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>3.700000e-18</td>\n",
       "      <td>74.9</td>\n",
       "      <td>2.3</td>\n",
       "      <td>2.300000e-17</td>\n",
       "      <td>72.3</td>\n",
       "      <td>2.3</td>\n",
       "      <td>D4998_C2223_H2</td>\n",
       "      <td>D4998_C2223_H2_Bin_329_scaffold_361784_9</td>\n",
       "      <td>...</td>\n",
       "      <td>D4998_C2223_H2_Bin_329</td>\n",
       "      <td>D4998_C2223_H2_Bin_329</td>\n",
       "      <td>d__Bacteria;p__Chloroflexota;c__Anaerolineae;o...</td>\n",
       "      <td>d__Bacteria</td>\n",
       "      <td>p__Chloroflexota</td>\n",
       "      <td>c__Anaerolineae</td>\n",
       "      <td>o__UBA1429</td>\n",
       "      <td>f__UBA1429</td>\n",
       "      <td>g__</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>212</th>\n",
       "      <td>D4993_C5_H3_Bin_412_scaffold_75643_3</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>3.900000e-17</td>\n",
       "      <td>71.5</td>\n",
       "      <td>1.9</td>\n",
       "      <td>1.000000e-16</td>\n",
       "      <td>70.2</td>\n",
       "      <td>1.9</td>\n",
       "      <td>D4993_C5_H3</td>\n",
       "      <td>D4993_C5_H3_Bin_412_scaffold_75643_3</td>\n",
       "      <td>...</td>\n",
       "      <td>D4993_C5_H3_Bin_412</td>\n",
       "      <td>D4993_C5_H3_Bin_412</td>\n",
       "      <td>d__Bacteria;p__Chloroflexota;c__Anaerolineae;o...</td>\n",
       "      <td>d__Bacteria</td>\n",
       "      <td>p__Chloroflexota</td>\n",
       "      <td>c__Anaerolineae</td>\n",
       "      <td>o__JADYZS01</td>\n",
       "      <td>f__JADYZS01</td>\n",
       "      <td>g__</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>299</th>\n",
       "      <td>D4993_C5_H1_Bin_313_scaffold_691639_41</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>1.700000e-14</td>\n",
       "      <td>62.9</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.400000e-14</td>\n",
       "      <td>61.9</td>\n",
       "      <td>0.0</td>\n",
       "      <td>D4993_C5_H1</td>\n",
       "      <td>D4993_C5_H1_Bin_313_scaffold_691639_41</td>\n",
       "      <td>...</td>\n",
       "      <td>D4993_C5_H1_Bin_313</td>\n",
       "      <td>D4993_C5_H1_Bin_313</td>\n",
       "      <td>d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__...</td>\n",
       "      <td>d__Bacteria</td>\n",
       "      <td>p__Bacteroidota</td>\n",
       "      <td>c__Bacteroidia</td>\n",
       "      <td>o__Bacteroidales</td>\n",
       "      <td>f__GWF2-38-335</td>\n",
       "      <td>g__</td>\n",
       "      <td>s__</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",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>261</th>\n",
       "      <td>D4993_C5_H1_Bin_235_scaffold_166170_7</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>4.000000e-05</td>\n",
       "      <td>32.2</td>\n",
       "      <td>0.0</td>\n",
       "      <td>6.100000e-05</td>\n",
       "      <td>31.5</td>\n",
       "      <td>0.0</td>\n",
       "      <td>D4993_C5_H1</td>\n",
       "      <td>D4993_C5_H1_Bin_235_scaffold_166170_7</td>\n",
       "      <td>...</td>\n",
       "      <td>D4993_C5_H1_Bin_235</td>\n",
       "      <td>D4993_C5_H1_Bin_235</td>\n",
       "      <td>d__Bacteria;p__Planctomycetota;c__Phycisphaera...</td>\n",
       "      <td>d__Bacteria</td>\n",
       "      <td>p__Planctomycetota</td>\n",
       "      <td>c__Phycisphaerae</td>\n",
       "      <td>o__</td>\n",
       "      <td>f__</td>\n",
       "      <td>g__</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>126</th>\n",
       "      <td>D4994_C39_H1_Bin_146_scaffold_636346_1</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>4.200000e-05</td>\n",
       "      <td>32.1</td>\n",
       "      <td>0.4</td>\n",
       "      <td>7.300000e+00</td>\n",
       "      <td>14.9</td>\n",
       "      <td>0.0</td>\n",
       "      <td>D4994_C39_H1</td>\n",
       "      <td>D4994_C39_H1_Bin_146_scaffold_636346_1</td>\n",
       "      <td>...</td>\n",
       "      <td>D4994_C39_H1_Bin_146</td>\n",
       "      <td>D4994_C39_H1_Bin_146</td>\n",
       "      <td>d__Bacteria;p__Armatimonadota;c__UBA5377;o__UB...</td>\n",
       "      <td>d__Bacteria</td>\n",
       "      <td>p__Armatimonadota</td>\n",
       "      <td>c__UBA5377</td>\n",
       "      <td>o__UBA5377</td>\n",
       "      <td>f__JABUFB01</td>\n",
       "      <td>g__JABUFB01</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>321</th>\n",
       "      <td>D4998_C2223_H2_Bin_339_scaffold_221503_1</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>4.300000e-05</td>\n",
       "      <td>32.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5.800000e-05</td>\n",
       "      <td>31.6</td>\n",
       "      <td>0.0</td>\n",
       "      <td>D4998_C2223_H2</td>\n",
       "      <td>D4998_C2223_H2_Bin_339_scaffold_221503_1</td>\n",
       "      <td>...</td>\n",
       "      <td>D4998_C2223_H2_Bin_339</td>\n",
       "      <td>D4998_C2223_H2_Bin_339</td>\n",
       "      <td>d__Bacteria;p__Pseudomonadota;c__Gammaproteoba...</td>\n",
       "      <td>d__Bacteria</td>\n",
       "      <td>p__Pseudomonadota</td>\n",
       "      <td>c__Gammaproteobacteria</td>\n",
       "      <td>o__Woeseiales</td>\n",
       "      <td>f__Woeseiaceae</td>\n",
       "      <td>g__SZUA-117</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>120</th>\n",
       "      <td>D4994_C39_H1_Bin_679_scaffold_476470_86</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>4.500000e-05</td>\n",
       "      <td>32.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.100000e-02</td>\n",
       "      <td>22.6</td>\n",
       "      <td>0.0</td>\n",
       "      <td>D4994_C39_H1</td>\n",
       "      <td>D4994_C39_H1_Bin_679_scaffold_476470_86</td>\n",
       "      <td>...</td>\n",
       "      <td>D4994_C39_H1_Bin_679</td>\n",
       "      <td>D4994_C39_H1_Bin_679</td>\n",
       "      <td>d__Bacteria;p__Planctomycetota;c__DG-23;o__;f_...</td>\n",
       "      <td>d__Bacteria</td>\n",
       "      <td>p__Planctomycetota</td>\n",
       "      <td>c__DG-23</td>\n",
       "      <td>o__</td>\n",
       "      <td>f__</td>\n",
       "      <td>g__</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>209</th>\n",
       "      <td>D4993_C5_H3_Bin_428_scaffold_410551_4</td>\n",
       "      <td>00129_Cutinase_Thermobifida_fusca_PET_muscle</td>\n",
       "      <td>4.700000e-05</td>\n",
       "      <td>31.9</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.600000e-04</td>\n",
       "      <td>30.2</td>\n",
       "      <td>0.0</td>\n",
       "      <td>D4993_C5_H3</td>\n",
       "      <td>D4993_C5_H3_Bin_428_scaffold_410551_4</td>\n",
       "      <td>...</td>\n",
       "      <td>D4993_C5_H3_Bin_428</td>\n",
       "      <td>D4993_C5_H3_Bin_428</td>\n",
       "      <td>d__Bacteria;p__Planctomycetota;c__Phycisphaera...</td>\n",
       "      <td>d__Bacteria</td>\n",
       "      <td>p__Planctomycetota</td>\n",
       "      <td>c__Phycisphaerae</td>\n",
       "      <td>o__SM23-33</td>\n",
       "      <td>f__SM23-33</td>\n",
       "      <td>g__MVCS01</td>\n",
       "      <td>s__</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>196 rows × 23 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                  target_name  \\\n",
       "272    D4993_C5_H1_Bin_524_scaffold_590470_15   \n",
       "158      D4993_C5_H4_Bin_238_scaffold_20386_9   \n",
       "332  D4998_C2223_H2_Bin_329_scaffold_361784_9   \n",
       "212      D4993_C5_H3_Bin_412_scaffold_75643_3   \n",
       "299    D4993_C5_H1_Bin_313_scaffold_691639_41   \n",
       "..                                        ...   \n",
       "261     D4993_C5_H1_Bin_235_scaffold_166170_7   \n",
       "126    D4994_C39_H1_Bin_146_scaffold_636346_1   \n",
       "321  D4998_C2223_H2_Bin_339_scaffold_221503_1   \n",
       "120   D4994_C39_H1_Bin_679_scaffold_476470_86   \n",
       "209     D4993_C5_H3_Bin_428_scaffold_410551_4   \n",
       "\n",
       "                                       query_name  full_sequence_evalue  \\\n",
       "272  00129_Cutinase_Thermobifida_fusca_PET_muscle          1.600000e-42   \n",
       "158  00129_Cutinase_Thermobifida_fusca_PET_muscle          2.100000e-20   \n",
       "332  00129_Cutinase_Thermobifida_fusca_PET_muscle          3.700000e-18   \n",
       "212  00129_Cutinase_Thermobifida_fusca_PET_muscle          3.900000e-17   \n",
       "299  00129_Cutinase_Thermobifida_fusca_PET_muscle          1.700000e-14   \n",
       "..                                            ...                   ...   \n",
       "261  00129_Cutinase_Thermobifida_fusca_PET_muscle          4.000000e-05   \n",
       "126  00129_Cutinase_Thermobifida_fusca_PET_muscle          4.200000e-05   \n",
       "321  00129_Cutinase_Thermobifida_fusca_PET_muscle          4.300000e-05   \n",
       "120  00129_Cutinase_Thermobifida_fusca_PET_muscle          4.500000e-05   \n",
       "209  00129_Cutinase_Thermobifida_fusca_PET_muscle          4.700000e-05   \n",
       "\n",
       "     full_sequence_score  full_sequence_bias  domain_e_evalue  domain_score  \\\n",
       "272                154.8                 7.8     3.500000e-12          55.3   \n",
       "158                 82.3                 0.1     2.900000e-20          81.8   \n",
       "332                 74.9                 2.3     2.300000e-17          72.3   \n",
       "212                 71.5                 1.9     1.000000e-16          70.2   \n",
       "299                 62.9                 0.0     3.400000e-14          61.9   \n",
       "..                   ...                 ...              ...           ...   \n",
       "261                 32.2                 0.0     6.100000e-05          31.5   \n",
       "126                 32.1                 0.4     7.300000e+00          14.9   \n",
       "321                 32.0                 0.0     5.800000e-05          31.6   \n",
       "120                 32.0                 0.0     3.100000e-02          22.6   \n",
       "209                 31.9                 0.0     1.600000e-04          30.2   \n",
       "\n",
       "     domain_bias            dive                                 ProteinID  \\\n",
       "272          0.3     D4993_C5_H1    D4993_C5_H1_Bin_524_scaffold_590470_15   \n",
       "158          0.1     D4993_C5_H4      D4993_C5_H4_Bin_238_scaffold_20386_9   \n",
       "332          2.3  D4998_C2223_H2  D4998_C2223_H2_Bin_329_scaffold_361784_9   \n",
       "212          1.9     D4993_C5_H3      D4993_C5_H3_Bin_412_scaffold_75643_3   \n",
       "299          0.0     D4993_C5_H1    D4993_C5_H1_Bin_313_scaffold_691639_41   \n",
       "..           ...             ...                                       ...   \n",
       "261          0.0     D4993_C5_H1     D4993_C5_H1_Bin_235_scaffold_166170_7   \n",
       "126          0.0    D4994_C39_H1    D4994_C39_H1_Bin_146_scaffold_636346_1   \n",
       "321          0.0  D4998_C2223_H2  D4998_C2223_H2_Bin_339_scaffold_221503_1   \n",
       "120          0.0    D4994_C39_H1   D4994_C39_H1_Bin_679_scaffold_476470_86   \n",
       "209          0.0     D4993_C5_H3     D4993_C5_H3_Bin_428_scaffold_410551_4   \n",
       "\n",
       "     ...                     Bin             user_genome  \\\n",
       "272  ...     D4993_C5_H1_Bin_524     D4993_C5_H1_Bin_524   \n",
       "158  ...     D4993_C5_H4_Bin_238     D4993_C5_H4_Bin_238   \n",
       "332  ...  D4998_C2223_H2_Bin_329  D4998_C2223_H2_Bin_329   \n",
       "212  ...     D4993_C5_H3_Bin_412     D4993_C5_H3_Bin_412   \n",
       "299  ...     D4993_C5_H1_Bin_313     D4993_C5_H1_Bin_313   \n",
       "..   ...                     ...                     ...   \n",
       "261  ...     D4993_C5_H1_Bin_235     D4993_C5_H1_Bin_235   \n",
       "126  ...    D4994_C39_H1_Bin_146    D4994_C39_H1_Bin_146   \n",
       "321  ...  D4998_C2223_H2_Bin_339  D4998_C2223_H2_Bin_339   \n",
       "120  ...    D4994_C39_H1_Bin_679    D4994_C39_H1_Bin_679   \n",
       "209  ...     D4993_C5_H3_Bin_428     D4993_C5_H3_Bin_428   \n",
       "\n",
       "                                        classification      level_0  \\\n",
       "272  d__Bacteria;p__Chloroflexota;c__Anaerolineae;o...  d__Bacteria   \n",
       "158  d__Archaea;p__Thermoproteota;c__Bathyarchaeia;...   d__Archaea   \n",
       "332  d__Bacteria;p__Chloroflexota;c__Anaerolineae;o...  d__Bacteria   \n",
       "212  d__Bacteria;p__Chloroflexota;c__Anaerolineae;o...  d__Bacteria   \n",
       "299  d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__...  d__Bacteria   \n",
       "..                                                 ...          ...   \n",
       "261  d__Bacteria;p__Planctomycetota;c__Phycisphaera...  d__Bacteria   \n",
       "126  d__Bacteria;p__Armatimonadota;c__UBA5377;o__UB...  d__Bacteria   \n",
       "321  d__Bacteria;p__Pseudomonadota;c__Gammaproteoba...  d__Bacteria   \n",
       "120  d__Bacteria;p__Planctomycetota;c__DG-23;o__;f_...  d__Bacteria   \n",
       "209  d__Bacteria;p__Planctomycetota;c__Phycisphaera...  d__Bacteria   \n",
       "\n",
       "                level_1                 level_2           level_3  \\\n",
       "272    p__Chloroflexota         c__Anaerolineae       o__JAFGEY01   \n",
       "158   p__Thermoproteota        c__Bathyarchaeia          o__B26-1   \n",
       "332    p__Chloroflexota         c__Anaerolineae        o__UBA1429   \n",
       "212    p__Chloroflexota         c__Anaerolineae       o__JADYZS01   \n",
       "299     p__Bacteroidota          c__Bacteroidia  o__Bacteroidales   \n",
       "..                  ...                     ...               ...   \n",
       "261  p__Planctomycetota        c__Phycisphaerae               o__   \n",
       "126   p__Armatimonadota              c__UBA5377        o__UBA5377   \n",
       "321   p__Pseudomonadota  c__Gammaproteobacteria     o__Woeseiales   \n",
       "120  p__Planctomycetota                c__DG-23               o__   \n",
       "209  p__Planctomycetota        c__Phycisphaerae        o__SM23-33   \n",
       "\n",
       "            level_4      level_5 level_6  \n",
       "272     f__JAFGEY01          g__     s__  \n",
       "158       f__WUQV01          g__     s__  \n",
       "332      f__UBA1429          g__     s__  \n",
       "212     f__JADYZS01          g__     s__  \n",
       "299  f__GWF2-38-335          g__     s__  \n",
       "..              ...          ...     ...  \n",
       "261             f__          g__     s__  \n",
       "126     f__JABUFB01  g__JABUFB01     s__  \n",
       "321  f__Woeseiaceae  g__SZUA-117     s__  \n",
       "120             f__          g__     s__  \n",
       "209      f__SM23-33    g__MVCS01     s__  \n",
       "\n",
       "[196 rows x 23 columns]"
      ]
     },
     "execution_count": 48,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pet_new_"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#write out a fasta file of all of the proteins\n",
    "pet_fp = '../../data/results/PETHits_uniqueclassification_Guaymas2020.fasta'\n",
    "with open(pet_fp, 'w') as f:\n",
    "    for seq in pet_new_[['target_name', 'aa_sequence']].values:\n",
    "        f.write('>' + seq[0] + '\\n')\n",
    "        f.write(seq[1] + '\\n')\n",
    "    f.close()\n",
    "\n",
    "#Choose candidates for further analysis from these unique phyla. "
   ]
  }
 ],
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