concat_genomes.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "f9fdc56f-e950-4879-80bd-500446edd9d8",
   "metadata": {},
   "outputs": [],
   "source": [
    "def parse_contig_number(header):\n",
    "    \"\"\"\n",
    "    Extracts the contig number from the header.\n",
    "    Example: \">NZ_JAEPPV010000006.1\" -> 6\n",
    "    \"\"\"\n",
    "    parts = header.split(\".\")\n",
    "    contig_number = int(parts[0].split(\"_\")[-1][6:])\n",
    "    return contig_number\n",
    "\n",
    "def process_fna_file(input_fna, concatenated_fna, sorted_concatenated_fna):\n",
    "    contigs = {}\n",
    "    current_header = None\n",
    "    current_sequence = []\n",
    "\n",
    "    # Read the file manually\n",
    "    with open(input_fna, \"r\") as file:\n",
    "        for line in file:\n",
    "            line = line.strip()\n",
    "            if line.startswith(\">\"):\n",
    "                if current_header:\n",
    "                    contigs[current_header] = ''.join(current_sequence)\n",
    "                current_header = line\n",
    "                current_sequence = []\n",
    "            else:\n",
    "                current_sequence.append(line)\n",
    "        if current_header:\n",
    "            contigs[current_header] = ''.join(current_sequence)\n",
    "\n",
    "    # Concatenate all contigs into one sequence\n",
    "    concatenated_seq = ''.join(contigs.values())\n",
    "\n",
    "    # Save the concatenated sequence to the first output file\n",
    "    with open(concatenated_fna, \"w\") as output_handle:\n",
    "        output_handle.write(\">concatenated_sequence\\n\")\n",
    "        output_handle.write(concatenated_seq + \"\\n\")\n",
    "\n",
    "    # Sort the contigs based on their contig number\n",
    "    sorted_contigs = sorted(contigs.items(), key=lambda x: parse_contig_number(x[0]))\n",
    "\n",
    "    # Concatenate the sorted contigs into one sequence\n",
    "    sorted_concatenated_seq = ''.join(seq for _, seq in sorted_contigs)\n",
    "\n",
    "    # Save the sorted concatenated sequence to the second output file\n",
    "    with open(sorted_concatenated_fna, \"w\") as output_handle:\n",
    "        output_handle.write(\">sorted_concatenated_sequence\\n\")\n",
    "        output_handle.write(sorted_concatenated_seq + \"\\n\")\n",
    "\n",
    "# Example usage:\n",
    "input_fna = \"10.fna\"  # Replace with your input file name\n",
    "concatenated_fna = \"concatenated_contigs.fna\"\n",
    "sorted_concatenated_fna = \"sorted_concatenated_contigs.fna\"\n",
    "\n",
    "process_fna_file(input_fna, concatenated_fna, sorted_concatenated_fna)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "e1cd3b7b-75c5-478d-9960-2cde8e7f3e4c",
   "metadata": {},
   "outputs": [],
   "source": [
    "def extract_first_n_contigs(input_fna, output_fna, n=5):\n",
    "    \"\"\"\n",
    "    Extract the first n contigs from an input .fna file and write them to a new file.\n",
    "    \n",
    "    Parameters:\n",
    "    - input_fna: Path to the input .fna file.\n",
    "    - output_fna: Path to the output .fna file.\n",
    "    - n: Number of contigs to extract (default is 5).\n",
    "    \"\"\"\n",
    "    contig_count = 0\n",
    "    with open(input_fna, \"r\") as infile, open(output_fna, \"w\") as outfile:\n",
    "        for line in infile:\n",
    "            if line.startswith(\">\"):\n",
    "                contig_count += 1\n",
    "                if contig_count > n:\n",
    "                    break\n",
    "            outfile.write(line)\n",
    "\n",
    "# Example usage:\n",
    "input_fna = \"38.fna\"  # Replace with your actual input file\n",
    "output_fna = \"5.fna\"\n",
    "\n",
    "extract_first_n_contigs(input_fna, output_fna, n=5)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "a71735ff-c53d-4235-ad2f-38ae3b781543",
   "metadata": {},
   "outputs": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>query_id</th>\n",
       "      <th>subject_id</th>\n",
       "      <th>perc_identity</th>\n",
       "      <th>alignment_length</th>\n",
       "      <th>mismatches</th>\n",
       "      <th>gaps</th>\n",
       "      <th>q_start</th>\n",
       "      <th>q_end</th>\n",
       "      <th>s_start</th>\n",
       "      <th>s_end</th>\n",
       "      <th>evalue</th>\n",
       "      <th>bit_score</th>\n",
       "      <th>qcov</th>\n",
       "      <th>qcovhsp</th>\n",
       "      <th>qlen</th>\n",
       "      <th>slen</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>NZ_JAEPPV010000003.1</td>\n",
       "      <td>75.690</td>\n",
       "      <td>11493</td>\n",
       "      <td>2460</td>\n",
       "      <td>334</td>\n",
       "      <td>394896</td>\n",
       "      <td>406227</td>\n",
       "      <td>27515</td>\n",
       "      <td>38834</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>5437.0</td>\n",
       "      <td>6</td>\n",
       "      <td>2</td>\n",
       "      <td>646567</td>\n",
       "      <td>460968</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>NZ_JAEPPV010000003.1</td>\n",
       "      <td>85.645</td>\n",
       "      <td>2271</td>\n",
       "      <td>288</td>\n",
       "      <td>38</td>\n",
       "      <td>372787</td>\n",
       "      <td>375043</td>\n",
       "      <td>15346</td>\n",
       "      <td>17592</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>2353.0</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>646567</td>\n",
       "      <td>460968</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>NZ_JAEPPV010000003.1</td>\n",
       "      <td>80.080</td>\n",
       "      <td>2505</td>\n",
       "      <td>476</td>\n",
       "      <td>23</td>\n",
       "      <td>557989</td>\n",
       "      <td>560480</td>\n",
       "      <td>351254</td>\n",
       "      <td>353748</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>1840.0</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>646567</td>\n",
       "      <td>460968</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>NZ_JAEPPV010000003.1</td>\n",
       "      <td>74.885</td>\n",
       "      <td>3699</td>\n",
       "      <td>819</td>\n",
       "      <td>110</td>\n",
       "      <td>433985</td>\n",
       "      <td>437629</td>\n",
       "      <td>61383</td>\n",
       "      <td>65025</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>1583.0</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>646567</td>\n",
       "      <td>460968</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>NZ_JAEPPV010000003.1</td>\n",
       "      <td>77.516</td>\n",
       "      <td>2415</td>\n",
       "      <td>523</td>\n",
       "      <td>20</td>\n",
       "      <td>440547</td>\n",
       "      <td>442951</td>\n",
       "      <td>69678</td>\n",
       "      <td>72082</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>1434.0</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>646567</td>\n",
       "      <td>460968</td>\n",
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       "    <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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>204</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>NZ_JAEPPV010000001.1</td>\n",
       "      <td>77.025</td>\n",
       "      <td>605</td>\n",
       "      <td>120</td>\n",
       "      <td>19</td>\n",
       "      <td>42712</td>\n",
       "      <td>43309</td>\n",
       "      <td>571136</td>\n",
       "      <td>570544</td>\n",
       "      <td>2.010000e-88</td>\n",
       "      <td>329.0</td>\n",
       "      <td>27</td>\n",
       "      <td>1</td>\n",
       "      <td>117204</td>\n",
       "      <td>1120828</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>205</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>NZ_JAEPPV010000001.1</td>\n",
       "      <td>74.571</td>\n",
       "      <td>641</td>\n",
       "      <td>157</td>\n",
       "      <td>6</td>\n",
       "      <td>39189</td>\n",
       "      <td>39826</td>\n",
       "      <td>575763</td>\n",
       "      <td>575126</td>\n",
       "      <td>2.660000e-72</td>\n",
       "      <td>276.0</td>\n",
       "      <td>27</td>\n",
       "      <td>1</td>\n",
       "      <td>117204</td>\n",
       "      <td>1120828</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>206</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>NZ_JAEPPV010000001.1</td>\n",
       "      <td>80.460</td>\n",
       "      <td>348</td>\n",
       "      <td>43</td>\n",
       "      <td>25</td>\n",
       "      <td>2444</td>\n",
       "      <td>2769</td>\n",
       "      <td>612714</td>\n",
       "      <td>612370</td>\n",
       "      <td>2.700000e-62</td>\n",
       "      <td>243.0</td>\n",
       "      <td>27</td>\n",
       "      <td>0</td>\n",
       "      <td>117204</td>\n",
       "      <td>1120828</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>207</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>NZ_JAEPPV010000001.1</td>\n",
       "      <td>100.000</td>\n",
       "      <td>78</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>114083</td>\n",
       "      <td>114160</td>\n",
       "      <td>508082</td>\n",
       "      <td>508005</td>\n",
       "      <td>7.830000e-33</td>\n",
       "      <td>145.0</td>\n",
       "      <td>27</td>\n",
       "      <td>0</td>\n",
       "      <td>117204</td>\n",
       "      <td>1120828</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>208</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>NZ_JAEPPV010000003.1</td>\n",
       "      <td>73.262</td>\n",
       "      <td>374</td>\n",
       "      <td>81</td>\n",
       "      <td>19</td>\n",
       "      <td>106241</td>\n",
       "      <td>106600</td>\n",
       "      <td>392956</td>\n",
       "      <td>392588</td>\n",
       "      <td>4.750000e-25</td>\n",
       "      <td>119.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>117204</td>\n",
       "      <td>460968</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>209 rows × 16 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "         query_id            subject_id  perc_identity  alignment_length  \\\n",
       "0    AWFD01000001  NZ_JAEPPV010000003.1         75.690             11493   \n",
       "1    AWFD01000001  NZ_JAEPPV010000003.1         85.645              2271   \n",
       "2    AWFD01000001  NZ_JAEPPV010000003.1         80.080              2505   \n",
       "3    AWFD01000001  NZ_JAEPPV010000003.1         74.885              3699   \n",
       "4    AWFD01000001  NZ_JAEPPV010000003.1         77.516              2415   \n",
       "..            ...                   ...            ...               ...   \n",
       "204  AWFD01000005  NZ_JAEPPV010000001.1         77.025               605   \n",
       "205  AWFD01000005  NZ_JAEPPV010000001.1         74.571               641   \n",
       "206  AWFD01000005  NZ_JAEPPV010000001.1         80.460               348   \n",
       "207  AWFD01000005  NZ_JAEPPV010000001.1        100.000                78   \n",
       "208  AWFD01000005  NZ_JAEPPV010000003.1         73.262               374   \n",
       "\n",
       "     mismatches  gaps  q_start   q_end  s_start   s_end        evalue  \\\n",
       "0          2460   334   394896  406227    27515   38834  0.000000e+00   \n",
       "1           288    38   372787  375043    15346   17592  0.000000e+00   \n",
       "2           476    23   557989  560480   351254  353748  0.000000e+00   \n",
       "3           819   110   433985  437629    61383   65025  0.000000e+00   \n",
       "4           523    20   440547  442951    69678   72082  0.000000e+00   \n",
       "..          ...   ...      ...     ...      ...     ...           ...   \n",
       "204         120    19    42712   43309   571136  570544  2.010000e-88   \n",
       "205         157     6    39189   39826   575763  575126  2.660000e-72   \n",
       "206          43    25     2444    2769   612714  612370  2.700000e-62   \n",
       "207           0     0   114083  114160   508082  508005  7.830000e-33   \n",
       "208          81    19   106241  106600   392956  392588  4.750000e-25   \n",
       "\n",
       "     bit_score  qcov  qcovhsp    qlen     slen  \n",
       "0       5437.0     6        2  646567   460968  \n",
       "1       2353.0     6        0  646567   460968  \n",
       "2       1840.0     6        0  646567   460968  \n",
       "3       1583.0     6        1  646567   460968  \n",
       "4       1434.0     6        0  646567   460968  \n",
       "..         ...   ...      ...     ...      ...  \n",
       "204      329.0    27        1  117204  1120828  \n",
       "205      276.0    27        1  117204  1120828  \n",
       "206      243.0    27        0  117204  1120828  \n",
       "207      145.0    27        0  117204  1120828  \n",
       "208      119.0     0        0  117204   460968  \n",
       "\n",
       "[209 rows x 16 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import pandas as pd\n",
    "\n",
    "# Define the column names based on the format of the BLAST output.\n",
    "# The default BLAST tabular output (-outfmt 6) has these columns:\n",
    "column_names = [\n",
    "    \"query_id\", \"subject_id\", \"perc_identity\", \"alignment_length\", \"mismatches\",\n",
    "    \"gaps\", \"q_start\", \"q_end\", \"s_start\", \"s_end\", \"evalue\", \"bit_score\", \"qcov\", \"qcovhsp\", \"qlen\", \"slen\"\n",
    "]\n",
    "\n",
    "# Read the BLAST output file into a pandas DataFrame\n",
    "blast_output_file1 = \"output_5_to_10.blast\"\n",
    "blast_output_file2 = \"output_5_to_concat10.blast\"\n",
    "blast_output_file3 = \"output_5_to_sorted_concat10.blast\"# Replace with your BLAST output file\n",
    "default_df = pd.read_csv(blast_output_file1, sep=\"\\t\", header=None, names=column_names)\n",
    "concat_df = pd.read_csv(blast_output_file2, sep=\"\\t\", header=None, names=column_names)\n",
    "sorted_concat_df = pd.read_csv(blast_output_file3, sep=\"\\t\", header=None, names=column_names)\n",
    "# Display the first few rows of the DataFrame\n",
    "default_df\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "923c9098-fb26-4918-a72f-3177b8681c5a",
   "metadata": {},
   "outputs": [
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>query_id</th>\n",
       "      <th>subject_id</th>\n",
       "      <th>perc_identity</th>\n",
       "      <th>alignment_length</th>\n",
       "      <th>mismatches</th>\n",
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       "      <th>qcov</th>\n",
       "      <th>qcovhsp</th>\n",
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       "      <th>slen</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>75.692</td>\n",
       "      <td>11494</td>\n",
       "      <td>2458</td>\n",
       "      <td>336</td>\n",
       "      <td>394896</td>\n",
       "      <td>406227</td>\n",
       "      <td>488111</td>\n",
       "      <td>499430</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>5437.0</td>\n",
       "      <td>30</td>\n",
       "      <td>2</td>\n",
       "      <td>646567</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>74.691</td>\n",
       "      <td>8973</td>\n",
       "      <td>2046</td>\n",
       "      <td>225</td>\n",
       "      <td>151122</td>\n",
       "      <td>159977</td>\n",
       "      <td>94669</td>\n",
       "      <td>103533</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>3781.0</td>\n",
       "      <td>30</td>\n",
       "      <td>1</td>\n",
       "      <td>646567</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>82.442</td>\n",
       "      <td>3292</td>\n",
       "      <td>510</td>\n",
       "      <td>68</td>\n",
       "      <td>45310</td>\n",
       "      <td>48571</td>\n",
       "      <td>176321</td>\n",
       "      <td>179574</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>2815.0</td>\n",
       "      <td>30</td>\n",
       "      <td>1</td>\n",
       "      <td>646567</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>80.768</td>\n",
       "      <td>3567</td>\n",
       "      <td>612</td>\n",
       "      <td>74</td>\n",
       "      <td>140848</td>\n",
       "      <td>144384</td>\n",
       "      <td>86886</td>\n",
       "      <td>90408</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>2719.0</td>\n",
       "      <td>30</td>\n",
       "      <td>1</td>\n",
       "      <td>646567</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>80.213</td>\n",
       "      <td>3376</td>\n",
       "      <td>581</td>\n",
       "      <td>87</td>\n",
       "      <td>86964</td>\n",
       "      <td>90299</td>\n",
       "      <td>218117</td>\n",
       "      <td>221445</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>2453.0</td>\n",
       "      <td>30</td>\n",
       "      <td>1</td>\n",
       "      <td>646567</td>\n",
       "      <td>3327926</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>204</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>77.025</td>\n",
       "      <td>605</td>\n",
       "      <td>120</td>\n",
       "      <td>19</td>\n",
       "      <td>42712</td>\n",
       "      <td>43309</td>\n",
       "      <td>1903186</td>\n",
       "      <td>1902594</td>\n",
       "      <td>2.010000e-88</td>\n",
       "      <td>329.0</td>\n",
       "      <td>27</td>\n",
       "      <td>1</td>\n",
       "      <td>117204</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>205</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>74.571</td>\n",
       "      <td>641</td>\n",
       "      <td>157</td>\n",
       "      <td>6</td>\n",
       "      <td>39189</td>\n",
       "      <td>39826</td>\n",
       "      <td>1907813</td>\n",
       "      <td>1907176</td>\n",
       "      <td>2.660000e-72</td>\n",
       "      <td>276.0</td>\n",
       "      <td>27</td>\n",
       "      <td>1</td>\n",
       "      <td>117204</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>206</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>80.460</td>\n",
       "      <td>348</td>\n",
       "      <td>43</td>\n",
       "      <td>25</td>\n",
       "      <td>2444</td>\n",
       "      <td>2769</td>\n",
       "      <td>1944764</td>\n",
       "      <td>1944420</td>\n",
       "      <td>2.700000e-62</td>\n",
       "      <td>243.0</td>\n",
       "      <td>27</td>\n",
       "      <td>0</td>\n",
       "      <td>117204</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>207</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>100.000</td>\n",
       "      <td>78</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>114083</td>\n",
       "      <td>114160</td>\n",
       "      <td>1840132</td>\n",
       "      <td>1840055</td>\n",
       "      <td>7.830000e-33</td>\n",
       "      <td>145.0</td>\n",
       "      <td>27</td>\n",
       "      <td>0</td>\n",
       "      <td>117204</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>208</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>73.262</td>\n",
       "      <td>374</td>\n",
       "      <td>81</td>\n",
       "      <td>19</td>\n",
       "      <td>106241</td>\n",
       "      <td>106600</td>\n",
       "      <td>853552</td>\n",
       "      <td>853184</td>\n",
       "      <td>4.750000e-25</td>\n",
       "      <td>119.0</td>\n",
       "      <td>27</td>\n",
       "      <td>0</td>\n",
       "      <td>117204</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>209 rows × 16 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "         query_id             subject_id  perc_identity  alignment_length  \\\n",
       "0    AWFD01000001  concatenated_sequence         75.692             11494   \n",
       "1    AWFD01000001  concatenated_sequence         74.691              8973   \n",
       "2    AWFD01000001  concatenated_sequence         82.442              3292   \n",
       "3    AWFD01000001  concatenated_sequence         80.768              3567   \n",
       "4    AWFD01000001  concatenated_sequence         80.213              3376   \n",
       "..            ...                    ...            ...               ...   \n",
       "204  AWFD01000005  concatenated_sequence         77.025               605   \n",
       "205  AWFD01000005  concatenated_sequence         74.571               641   \n",
       "206  AWFD01000005  concatenated_sequence         80.460               348   \n",
       "207  AWFD01000005  concatenated_sequence        100.000                78   \n",
       "208  AWFD01000005  concatenated_sequence         73.262               374   \n",
       "\n",
       "     mismatches  gaps  q_start   q_end  s_start    s_end        evalue  \\\n",
       "0          2458   336   394896  406227   488111   499430  0.000000e+00   \n",
       "1          2046   225   151122  159977    94669   103533  0.000000e+00   \n",
       "2           510    68    45310   48571   176321   179574  0.000000e+00   \n",
       "3           612    74   140848  144384    86886    90408  0.000000e+00   \n",
       "4           581    87    86964   90299   218117   221445  0.000000e+00   \n",
       "..          ...   ...      ...     ...      ...      ...           ...   \n",
       "204         120    19    42712   43309  1903186  1902594  2.010000e-88   \n",
       "205         157     6    39189   39826  1907813  1907176  2.660000e-72   \n",
       "206          43    25     2444    2769  1944764  1944420  2.700000e-62   \n",
       "207           0     0   114083  114160  1840132  1840055  7.830000e-33   \n",
       "208          81    19   106241  106600   853552   853184  4.750000e-25   \n",
       "\n",
       "     bit_score  qcov  qcovhsp    qlen     slen  \n",
       "0       5437.0    30        2  646567  3327926  \n",
       "1       3781.0    30        1  646567  3327926  \n",
       "2       2815.0    30        1  646567  3327926  \n",
       "3       2719.0    30        1  646567  3327926  \n",
       "4       2453.0    30        1  646567  3327926  \n",
       "..         ...   ...      ...     ...      ...  \n",
       "204      329.0    27        1  117204  3327926  \n",
       "205      276.0    27        1  117204  3327926  \n",
       "206      243.0    27        0  117204  3327926  \n",
       "207      145.0    27        0  117204  3327926  \n",
       "208      119.0    27        0  117204  3327926  \n",
       "\n",
       "[209 rows x 16 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "concat_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "e824a661-8014-4693-8a33-b64e0ac5669a",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<div>\n",
       "<style scoped>\n",
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       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>query_id</th>\n",
       "      <th>subject_id</th>\n",
       "      <th>perc_identity</th>\n",
       "      <th>alignment_length</th>\n",
       "      <th>mismatches</th>\n",
       "      <th>gaps</th>\n",
       "      <th>q_start</th>\n",
       "      <th>q_end</th>\n",
       "      <th>s_start</th>\n",
       "      <th>s_end</th>\n",
       "      <th>evalue</th>\n",
       "      <th>bit_score</th>\n",
       "      <th>qcov</th>\n",
       "      <th>qcovhsp</th>\n",
       "      <th>qlen</th>\n",
       "      <th>slen</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>sorted_concatenated_sequence</td>\n",
       "      <td>75.690</td>\n",
       "      <td>11493</td>\n",
       "      <td>2460</td>\n",
       "      <td>334</td>\n",
       "      <td>394896</td>\n",
       "      <td>406227</td>\n",
       "      <td>1787348</td>\n",
       "      <td>1798667</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>5437.0</td>\n",
       "      <td>30</td>\n",
       "      <td>2</td>\n",
       "      <td>646567</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>sorted_concatenated_sequence</td>\n",
       "      <td>74.691</td>\n",
       "      <td>8973</td>\n",
       "      <td>2046</td>\n",
       "      <td>225</td>\n",
       "      <td>151122</td>\n",
       "      <td>159977</td>\n",
       "      <td>3132916</td>\n",
       "      <td>3141780</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>3781.0</td>\n",
       "      <td>30</td>\n",
       "      <td>1</td>\n",
       "      <td>646567</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>sorted_concatenated_sequence</td>\n",
       "      <td>82.442</td>\n",
       "      <td>3292</td>\n",
       "      <td>510</td>\n",
       "      <td>68</td>\n",
       "      <td>45310</td>\n",
       "      <td>48571</td>\n",
       "      <td>2753972</td>\n",
       "      <td>2757225</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>2815.0</td>\n",
       "      <td>30</td>\n",
       "      <td>1</td>\n",
       "      <td>646567</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>sorted_concatenated_sequence</td>\n",
       "      <td>80.768</td>\n",
       "      <td>3567</td>\n",
       "      <td>612</td>\n",
       "      <td>74</td>\n",
       "      <td>140848</td>\n",
       "      <td>144384</td>\n",
       "      <td>3125133</td>\n",
       "      <td>3128655</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>2719.0</td>\n",
       "      <td>30</td>\n",
       "      <td>1</td>\n",
       "      <td>646567</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>sorted_concatenated_sequence</td>\n",
       "      <td>80.213</td>\n",
       "      <td>3376</td>\n",
       "      <td>581</td>\n",
       "      <td>87</td>\n",
       "      <td>86964</td>\n",
       "      <td>90299</td>\n",
       "      <td>2795768</td>\n",
       "      <td>2799096</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>2453.0</td>\n",
       "      <td>30</td>\n",
       "      <td>1</td>\n",
       "      <td>646567</td>\n",
       "      <td>3327926</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>204</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>sorted_concatenated_sequence</td>\n",
       "      <td>77.025</td>\n",
       "      <td>605</td>\n",
       "      <td>120</td>\n",
       "      <td>19</td>\n",
       "      <td>42712</td>\n",
       "      <td>43309</td>\n",
       "      <td>571136</td>\n",
       "      <td>570544</td>\n",
       "      <td>2.010000e-88</td>\n",
       "      <td>329.0</td>\n",
       "      <td>27</td>\n",
       "      <td>1</td>\n",
       "      <td>117204</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>205</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>sorted_concatenated_sequence</td>\n",
       "      <td>74.571</td>\n",
       "      <td>641</td>\n",
       "      <td>157</td>\n",
       "      <td>6</td>\n",
       "      <td>39189</td>\n",
       "      <td>39826</td>\n",
       "      <td>575763</td>\n",
       "      <td>575126</td>\n",
       "      <td>2.660000e-72</td>\n",
       "      <td>276.0</td>\n",
       "      <td>27</td>\n",
       "      <td>1</td>\n",
       "      <td>117204</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>206</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>sorted_concatenated_sequence</td>\n",
       "      <td>80.460</td>\n",
       "      <td>348</td>\n",
       "      <td>43</td>\n",
       "      <td>25</td>\n",
       "      <td>2444</td>\n",
       "      <td>2769</td>\n",
       "      <td>612714</td>\n",
       "      <td>612370</td>\n",
       "      <td>2.700000e-62</td>\n",
       "      <td>243.0</td>\n",
       "      <td>27</td>\n",
       "      <td>0</td>\n",
       "      <td>117204</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>207</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>sorted_concatenated_sequence</td>\n",
       "      <td>100.000</td>\n",
       "      <td>78</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>114083</td>\n",
       "      <td>114160</td>\n",
       "      <td>508082</td>\n",
       "      <td>508005</td>\n",
       "      <td>7.830000e-33</td>\n",
       "      <td>145.0</td>\n",
       "      <td>27</td>\n",
       "      <td>0</td>\n",
       "      <td>117204</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>208</th>\n",
       "      <td>AWFD01000005</td>\n",
       "      <td>sorted_concatenated_sequence</td>\n",
       "      <td>73.262</td>\n",
       "      <td>374</td>\n",
       "      <td>81</td>\n",
       "      <td>19</td>\n",
       "      <td>106241</td>\n",
       "      <td>106600</td>\n",
       "      <td>2152789</td>\n",
       "      <td>2152421</td>\n",
       "      <td>4.750000e-25</td>\n",
       "      <td>119.0</td>\n",
       "      <td>27</td>\n",
       "      <td>0</td>\n",
       "      <td>117204</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>209 rows × 16 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "         query_id                    subject_id  perc_identity  \\\n",
       "0    AWFD01000001  sorted_concatenated_sequence         75.690   \n",
       "1    AWFD01000001  sorted_concatenated_sequence         74.691   \n",
       "2    AWFD01000001  sorted_concatenated_sequence         82.442   \n",
       "3    AWFD01000001  sorted_concatenated_sequence         80.768   \n",
       "4    AWFD01000001  sorted_concatenated_sequence         80.213   \n",
       "..            ...                           ...            ...   \n",
       "204  AWFD01000005  sorted_concatenated_sequence         77.025   \n",
       "205  AWFD01000005  sorted_concatenated_sequence         74.571   \n",
       "206  AWFD01000005  sorted_concatenated_sequence         80.460   \n",
       "207  AWFD01000005  sorted_concatenated_sequence        100.000   \n",
       "208  AWFD01000005  sorted_concatenated_sequence         73.262   \n",
       "\n",
       "     alignment_length  mismatches  gaps  q_start   q_end  s_start    s_end  \\\n",
       "0               11493        2460   334   394896  406227  1787348  1798667   \n",
       "1                8973        2046   225   151122  159977  3132916  3141780   \n",
       "2                3292         510    68    45310   48571  2753972  2757225   \n",
       "3                3567         612    74   140848  144384  3125133  3128655   \n",
       "4                3376         581    87    86964   90299  2795768  2799096   \n",
       "..                ...         ...   ...      ...     ...      ...      ...   \n",
       "204               605         120    19    42712   43309   571136   570544   \n",
       "205               641         157     6    39189   39826   575763   575126   \n",
       "206               348          43    25     2444    2769   612714   612370   \n",
       "207                78           0     0   114083  114160   508082   508005   \n",
       "208               374          81    19   106241  106600  2152789  2152421   \n",
       "\n",
       "           evalue  bit_score  qcov  qcovhsp    qlen     slen  \n",
       "0    0.000000e+00     5437.0    30        2  646567  3327926  \n",
       "1    0.000000e+00     3781.0    30        1  646567  3327926  \n",
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       "3    0.000000e+00     2719.0    30        1  646567  3327926  \n",
       "4    0.000000e+00     2453.0    30        1  646567  3327926  \n",
       "..            ...        ...   ...      ...     ...      ...  \n",
       "204  2.010000e-88      329.0    27        1  117204  3327926  \n",
       "205  2.660000e-72      276.0    27        1  117204  3327926  \n",
       "206  2.700000e-62      243.0    27        0  117204  3327926  \n",
       "207  7.830000e-33      145.0    27        0  117204  3327926  \n",
       "208  4.750000e-25      119.0    27        0  117204  3327926  \n",
       "\n",
       "[209 rows x 16 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sorted_concat_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "7241f3be-6dea-4ff3-a5e3-17d419ab1119",
   "metadata": {},
   "outputs": [],
   "source": [
    "default_df_sorted = default_df.sort_values(by=[\"perc_identity\", \"alignment_length\"], ascending=[False,False])\n",
    "default_df_sorted = default_df_sorted.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "167495bf-a21e-413b-89c9-8c0d4fac887d",
   "metadata": {},
   "outputs": [],
   "source": [
    "concat_df_sorted = concat_df.sort_values(by=[\"perc_identity\", \"alignment_length\"], ascending=[False,False])\n",
    "concat_df_sorted = concat_df_sorted.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "785eb828-ea0d-436d-bbe1-2701cc9b3adf",
   "metadata": {},
   "outputs": [],
   "source": [
    "concat_sorted_df_sorted = sorted_concat_df.sort_values(by=[\"perc_identity\", \"alignment_length\"], ascending=[False,False])\n",
    "concat_sorted_df_sorted = concat_sorted_df_sorted.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "636ef5a5-1cfb-44de-bd25-11b10de18653",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "False"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "default_df_sorted['index'].equals(concat_df_sorted['index'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "6b0bdad4-5575-4b22-b385-b4f41d0101b5",
   "metadata": {},
   "outputs": [],
   "source": [
    "mask = default_df_sorted != concat_df_sorted"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "id": "8236bba1-ef02-4668-9cc2-1878742eb63d",
   "metadata": {},
   "outputs": [
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       "     index  query_id  subject_id  perc_identity  alignment_length  mismatches  \\\n",
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       "..     ...       ...         ...            ...               ...         ...   \n",
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       "\n",
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       "[209 rows x 17 columns]"
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     "execution_count": 39,
     "metadata": {},
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   "source": [
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   "execution_count": 26,
   "id": "75e48a8e-0e2a-4eed-865a-a56a7a9e6dca",
   "metadata": {},
   "outputs": [
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       "      <td>NZ_JAEPPV010000006.1</td>\n",
       "      <td>72.333</td>\n",
       "      <td>900</td>\n",
       "      <td>217</td>\n",
       "      <td>32</td>\n",
       "      <td>24603</td>\n",
       "      <td>25486</td>\n",
       "      <td>39638</td>\n",
       "      <td>40521</td>\n",
       "      <td>6.880000e-65</td>\n",
       "      <td>254.0</td>\n",
       "      <td>7</td>\n",
       "      <td>0</td>\n",
       "      <td>646567</td>\n",
       "      <td>216801</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>205</th>\n",
       "      <td>132</td>\n",
       "      <td>AWFD01000002</td>\n",
       "      <td>NZ_JAEPPV010000005.1</td>\n",
       "      <td>71.229</td>\n",
       "      <td>1505</td>\n",
       "      <td>379</td>\n",
       "      <td>54</td>\n",
       "      <td>122807</td>\n",
       "      <td>124284</td>\n",
       "      <td>218893</td>\n",
       "      <td>220370</td>\n",
       "      <td>9.170000e-89</td>\n",
       "      <td>331.0</td>\n",
       "      <td>21</td>\n",
       "      <td>1</td>\n",
       "      <td>191994</td>\n",
       "      <td>236043</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>206</th>\n",
       "      <td>114</td>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>NZ_JAEPPV010000001.1</td>\n",
       "      <td>71.128</td>\n",
       "      <td>523</td>\n",
       "      <td>118</td>\n",
       "      <td>33</td>\n",
       "      <td>477021</td>\n",
       "      <td>477530</td>\n",
       "      <td>273001</td>\n",
       "      <td>273503</td>\n",
       "      <td>3.410000e-18</td>\n",
       "      <td>99.0</td>\n",
       "      <td>8</td>\n",
       "      <td>0</td>\n",
       "      <td>646567</td>\n",
       "      <td>1120828</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>207</th>\n",
       "      <td>56</td>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>NZ_JAEPPV010000006.1</td>\n",
       "      <td>70.676</td>\n",
       "      <td>1006</td>\n",
       "      <td>230</td>\n",
       "      <td>65</td>\n",
       "      <td>93256</td>\n",
       "      <td>94242</td>\n",
       "      <td>105620</td>\n",
       "      <td>106579</td>\n",
       "      <td>1.190000e-37</td>\n",
       "      <td>163.0</td>\n",
       "      <td>7</td>\n",
       "      <td>0</td>\n",
       "      <td>646567</td>\n",
       "      <td>216801</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>208</th>\n",
       "      <td>171</td>\n",
       "      <td>AWFD01000004</td>\n",
       "      <td>NZ_JAEPPV010000002.1</td>\n",
       "      <td>69.864</td>\n",
       "      <td>1032</td>\n",
       "      <td>283</td>\n",
       "      <td>28</td>\n",
       "      <td>59631</td>\n",
       "      <td>60648</td>\n",
       "      <td>461983</td>\n",
       "      <td>460966</td>\n",
       "      <td>1.180000e-36</td>\n",
       "      <td>158.0</td>\n",
       "      <td>9</td>\n",
       "      <td>1</td>\n",
       "      <td>137817</td>\n",
       "      <td>639005</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>209 rows × 17 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     index      query_id            subject_id  perc_identity  \\\n",
       "0      207  AWFD01000005  NZ_JAEPPV010000001.1        100.000   \n",
       "1       78  AWFD01000001  NZ_JAEPPV010000007.1         98.795   \n",
       "2      142  AWFD01000002  NZ_JAEPPV010000003.1         98.039   \n",
       "3      182  AWFD01000004  NZ_JAEPPV010000004.1         94.505   \n",
       "4      137  AWFD01000002  NZ_JAEPPV010000005.1         93.443   \n",
       "..     ...           ...                   ...            ...   \n",
       "204     55  AWFD01000001  NZ_JAEPPV010000006.1         72.333   \n",
       "205    132  AWFD01000002  NZ_JAEPPV010000005.1         71.229   \n",
       "206    114  AWFD01000001  NZ_JAEPPV010000001.1         71.128   \n",
       "207     56  AWFD01000001  NZ_JAEPPV010000006.1         70.676   \n",
       "208    171  AWFD01000004  NZ_JAEPPV010000002.1         69.864   \n",
       "\n",
       "     alignment_length  mismatches  gaps  q_start   q_end  s_start   s_end  \\\n",
       "0                  78           0     0   114083  114160   508082  508005   \n",
       "1                  83           0     1   590225  590306    59361   59443   \n",
       "2                  51           1     0        1      51   460887  460837   \n",
       "3                  91           5     0    59501   59591   171942  172032   \n",
       "4                 122           8     0   122392  122513   218470  218591   \n",
       "..                ...         ...   ...      ...     ...      ...     ...   \n",
       "204               900         217    32    24603   25486    39638   40521   \n",
       "205              1505         379    54   122807  124284   218893  220370   \n",
       "206               523         118    33   477021  477530   273001  273503   \n",
       "207              1006         230    65    93256   94242   105620  106579   \n",
       "208              1032         283    28    59631   60648   461983  460966   \n",
       "\n",
       "           evalue  bit_score  qcov  qcovhsp    qlen     slen  \n",
       "0    7.830000e-33      145.0    27        0  117204  1120828  \n",
       "1    1.200000e-32      147.0     2        0  646567   125019  \n",
       "2    6.100000e-16       89.8     1        0  191994   460968  \n",
       "3    1.190000e-31      141.0    12        0  137817   239583  \n",
       "4    9.780000e-44      182.0    21        0  191994   236043  \n",
       "..            ...        ...   ...      ...     ...      ...  \n",
       "204  6.880000e-65      254.0     7        0  646567   216801  \n",
       "205  9.170000e-89      331.0    21        1  191994   236043  \n",
       "206  3.410000e-18       99.0     8        0  646567  1120828  \n",
       "207  1.190000e-37      163.0     7        0  646567   216801  \n",
       "208  1.180000e-36      158.0     9        1  137817   639005  \n",
       "\n",
       "[209 rows x 17 columns]"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "default_df_sorted"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "4ed77f18-8895-4b07-abad-761d0f282cbd",
   "metadata": {},
   "outputs": [
    {
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       "      <th></th>\n",
       "      <th>index</th>\n",
       "      <th>query_id</th>\n",
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       "      <td>AWFD01000004</td>\n",
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       "      <td>91</td>\n",
       "      <td>5</td>\n",
       "      <td>0</td>\n",
       "      <td>59501</td>\n",
       "      <td>59591</td>\n",
       "      <td>1175939</td>\n",
       "      <td>1176029</td>\n",
       "      <td>1.190000e-31</td>\n",
       "      <td>141.0</td>\n",
       "      <td>21</td>\n",
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       "      <td>137817</td>\n",
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       "      <td>AWFD01000002</td>\n",
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       "      <td>9.780000e-44</td>\n",
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       "      <td>99.0</td>\n",
       "      <td>30</td>\n",
       "      <td>0</td>\n",
       "      <td>646567</td>\n",
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       "    <tr>\n",
       "      <th>207</th>\n",
       "      <td>108</td>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>70.676</td>\n",
       "      <td>1006</td>\n",
       "      <td>230</td>\n",
       "      <td>65</td>\n",
       "      <td>93256</td>\n",
       "      <td>94242</td>\n",
       "      <td>224396</td>\n",
       "      <td>225355</td>\n",
       "      <td>1.190000e-37</td>\n",
       "      <td>163.0</td>\n",
       "      <td>30</td>\n",
       "      <td>0</td>\n",
       "      <td>646567</td>\n",
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       "    <tr>\n",
       "      <th>208</th>\n",
       "      <td>184</td>\n",
       "      <td>AWFD01000004</td>\n",
       "      <td>concatenated_sequence</td>\n",
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       "      <td>1032</td>\n",
       "      <td>283</td>\n",
       "      <td>28</td>\n",
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       "      <td>1.180000e-36</td>\n",
       "      <td>158.0</td>\n",
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      ],
      "text/plain": [
       "     index      query_id             subject_id  perc_identity  \\\n",
       "0      207  AWFD01000005  concatenated_sequence        100.000   \n",
       "1      110  AWFD01000001  concatenated_sequence         98.795   \n",
       "2      142  AWFD01000002  concatenated_sequence         98.039   \n",
       "3      186  AWFD01000004  concatenated_sequence         94.505   \n",
       "4      140  AWFD01000002  concatenated_sequence         93.443   \n",
       "..     ...           ...                    ...            ...   \n",
       "204    103  AWFD01000001  concatenated_sequence         72.333   \n",
       "205    135  AWFD01000002  concatenated_sequence         71.229   \n",
       "206    115  AWFD01000001  concatenated_sequence         71.128   \n",
       "207    108  AWFD01000001  concatenated_sequence         70.676   \n",
       "208    184  AWFD01000004  concatenated_sequence         69.864   \n",
       "\n",
       "     alignment_length  mismatches  gaps  q_start   q_end  s_start    s_end  \\\n",
       "0                  78           0     0   114083  114160  1840132  1840055   \n",
       "1                  83           0     1   590225  590306   394938   395020   \n",
       "2                  51           1     0        1      51   921483   921433   \n",
       "3                  91           5     0    59501   59591  1175939  1176029   \n",
       "4                 122           8     0   122392  122513  3310353  3310474   \n",
       "..                ...         ...   ...      ...     ...      ...      ...   \n",
       "204               900         217    32    24603   25486   158414   159297   \n",
       "205              1505         379    54   122807  124284  3310776  3312253   \n",
       "206               523         118    33   477021  477530  1605051  1605553   \n",
       "207              1006         230    65    93256   94242   224396   225355   \n",
       "208              1032         283    28    59631   60648  2914861  2913844   \n",
       "\n",
       "           evalue  bit_score  qcov  qcovhsp    qlen     slen  \n",
       "0    7.830000e-33      145.0    27        0  117204  3327926  \n",
       "1    1.200000e-32      147.0    30        0  646567  3327926  \n",
       "2    6.100000e-16       89.8    26        0  191994  3327926  \n",
       "3    1.190000e-31      141.0    21        0  137817  3327926  \n",
       "4    9.780000e-44      182.0    26        0  191994  3327926  \n",
       "..            ...        ...   ...      ...     ...      ...  \n",
       "204  6.880000e-65      254.0    30        0  646567  3327926  \n",
       "205  9.170000e-89      331.0    26        1  191994  3327926  \n",
       "206  3.410000e-18       99.0    30        0  646567  3327926  \n",
       "207  1.190000e-37      163.0    30        0  646567  3327926  \n",
       "208  1.180000e-36      158.0    21        1  137817  3327926  \n",
       "\n",
       "[209 rows x 17 columns]"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "concat_df_sorted"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "60db313c-3efe-42e0-a705-8e7411c55044",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "False"
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     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "default_df_sorted['alignment_length'].equals(concat_df_sorted['alignment_length'])"
   ]
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  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "fde3f6e8-f0d2-48a7-8865-efe754934a6f",
   "metadata": {},
   "outputs": [
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       "index                                 83\n",
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       "subject_id          NZ_JAEPPV010000001.1\n",
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       "     index  query_id  subject_id  perc_identity  alignment_length  mismatches  \\\n",
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       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    index  query_id  subject_id  perc_identity  alignment_length  mismatches  \\\n",
       "82   True     False        True           True              True        True   \n",
       "\n",
       "    gaps  q_start  q_end  s_start  s_end  evalue  bit_score  qcov  qcovhsp  \\\n",
       "82  True    False  False    False  False   False      False  True    False   \n",
       "\n",
       "     qlen  slen  \n",
       "82  False  True  "
      ]
     },
     "execution_count": 45,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mask2[mask2['alignment_length']==True]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "id": "d02b44f5-c6b4-4469-b2b6-612b8a164643",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "index                                         15\n",
       "query_id                            AWFD01000001\n",
       "subject_id          sorted_concatenated_sequence\n",
       "perc_identity                             79.882\n",
       "alignment_length                            2376\n",
       "mismatches                                   427\n",
       "gaps                                          51\n",
       "q_start                                   204143\n",
       "q_end                                     206487\n",
       "s_start                                    14036\n",
       "s_end                                      16391\n",
       "evalue                                       0.0\n",
       "bit_score                                 1692.0\n",
       "qcov                                          30\n",
       "qcovhsp                                        0\n",
       "qlen                                      646567\n",
       "slen                                     3327926\n",
       "Name: 82, dtype: object"
      ]
     },
     "execution_count": 46,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "concat_sorted_df_sorted.loc[82]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "id": "73bf4b4b-70ee-4617-99ef-7f3c464d0f3d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "index                                          0\n",
       "query_id                            AWFD01000001\n",
       "subject_id          sorted_concatenated_sequence\n",
       "perc_identity                              75.69\n",
       "alignment_length                           11493\n",
       "mismatches                                  2460\n",
       "gaps                                         334\n",
       "q_start                                   394896\n",
       "q_end                                     406227\n",
       "s_start                                  1787348\n",
       "s_end                                    1798667\n",
       "evalue                                       0.0\n",
       "bit_score                                 5437.0\n",
       "qcov                                          30\n",
       "qcovhsp                                        2\n",
       "qlen                                      646567\n",
       "slen                                     3327926\n",
       "Name: 149, dtype: object"
      ]
     },
     "execution_count": 47,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "concat_sorted_df_sorted.loc[149]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "id": "e162d978-3d0f-4aa4-b1f5-5ec0ca8658e1",
   "metadata": {},
   "outputs": [],
   "source": [
    "def concatenate_fasta(input_fasta, output_fasta, output_header=\"concat_sequence\"):\n",
    "    \"\"\"\n",
    "    Concatenate all contigs from a FASTA file into a single sequence and write to a new FASTA file.\n",
    "    \n",
    "    Parameters:\n",
    "    - input_fasta: Path to the input FASTA file containing multiple contigs.\n",
    "    - output_fasta: Path to the output FASTA file where the concatenated sequence will be saved.\n",
    "    - output_header: Header for the concatenated sequence in the output file.\n",
    "    \"\"\"\n",
    "    with open(input_fasta, 'r') as infile, open(output_fasta, 'w') as outfile:\n",
    "        sequence = \"\"\n",
    "        \n",
    "        for line in infile:\n",
    "            if line.startswith(\">\"):\n",
    "                # Skip headers from input FASTA file\n",
    "                continue\n",
    "            else:\n",
    "                sequence += line.strip()  # Concatenate sequence lines\n",
    "        \n",
    "        # Write the concatenated sequence to the output file\n",
    "        outfile.write(f\">{output_header}\\n\")\n",
    "        outfile.write(\"\\n\".join(sequence[i:i+80] for i in range(0, len(sequence), 80)) + '\\n')\n",
    "\n",
    "# Example usage:\n",
    "input_fasta = \"5.fna\"  # Replace with your actual input file path\n",
    "output_fasta = \"concatenated_sequence.fna\"\n",
    "\n",
    "concatenate_fasta(input_fasta, output_fasta)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a4de24e4-3ee3-4a20-9c2b-043b3ca77a82",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "id": "034e138f-87f8-48a7-baa4-7e722671a713",
   "metadata": {},
   "outputs": [
    {
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       "      <th>query_id</th>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>82.279</td>\n",
       "      <td>5186</td>\n",
       "      <td>873</td>\n",
       "      <td>46</td>\n",
       "      <td>994229</td>\n",
       "      <td>999392</td>\n",
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       "      <td>2696619</td>\n",
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       "      <th>2</th>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
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       "      <td>5108</td>\n",
       "      <td>887</td>\n",
       "      <td>74</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>74.691</td>\n",
       "      <td>8973</td>\n",
       "      <td>2046</td>\n",
       "      <td>225</td>\n",
       "      <td>151122</td>\n",
       "      <td>159977</td>\n",
       "      <td>94669</td>\n",
       "      <td>103533</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>3781.0</td>\n",
       "      <td>28</td>\n",
       "      <td>1</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>78.603</td>\n",
       "      <td>4767</td>\n",
       "      <td>935</td>\n",
       "      <td>85</td>\n",
       "      <td>659559</td>\n",
       "      <td>664286</td>\n",
       "      <td>3106571</td>\n",
       "      <td>3111291</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>3073.0</td>\n",
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       "      <td>0</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>204</th>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>83.471</td>\n",
       "      <td>121</td>\n",
       "      <td>16</td>\n",
       "      <td>4</td>\n",
       "      <td>568589</td>\n",
       "      <td>568707</td>\n",
       "      <td>390401</td>\n",
       "      <td>390519</td>\n",
       "      <td>3.020000e-21</td>\n",
       "      <td>110.0</td>\n",
       "      <td>28</td>\n",
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       "      <td>1240583</td>\n",
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       "    <tr>\n",
       "      <th>205</th>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>89.873</td>\n",
       "      <td>79</td>\n",
       "      <td>5</td>\n",
       "      <td>3</td>\n",
       "      <td>920303</td>\n",
       "      <td>920378</td>\n",
       "      <td>741961</td>\n",
       "      <td>742039</td>\n",
       "      <td>6.550000e-18</td>\n",
       "      <td>99.0</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>206</th>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>71.128</td>\n",
       "      <td>523</td>\n",
       "      <td>118</td>\n",
       "      <td>33</td>\n",
       "      <td>477021</td>\n",
       "      <td>477530</td>\n",
       "      <td>1605051</td>\n",
       "      <td>1605553</td>\n",
       "      <td>6.550000e-18</td>\n",
       "      <td>99.0</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</td>\n",
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       "    <tr>\n",
       "      <th>207</th>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>98.039</td>\n",
       "      <td>51</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>646568</td>\n",
       "      <td>646618</td>\n",
       "      <td>921483</td>\n",
       "      <td>921433</td>\n",
       "      <td>3.940000e-15</td>\n",
       "      <td>89.8</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>208</th>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>75.796</td>\n",
       "      <td>157</td>\n",
       "      <td>36</td>\n",
       "      <td>2</td>\n",
       "      <td>1050035</td>\n",
       "      <td>1050190</td>\n",
       "      <td>1172170</td>\n",
       "      <td>1172015</td>\n",
       "      <td>8.530000e-12</td>\n",
       "      <td>78.7</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>209 rows × 16 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            query_id             subject_id  perc_identity  alignment_length  \\\n",
       "0    concat_sequence  concatenated_sequence         75.692             11494   \n",
       "1    concat_sequence  concatenated_sequence         82.279              5186   \n",
       "2    concat_sequence  concatenated_sequence         81.186              5108   \n",
       "3    concat_sequence  concatenated_sequence         74.691              8973   \n",
       "4    concat_sequence  concatenated_sequence         78.603              4767   \n",
       "..               ...                    ...            ...               ...   \n",
       "204  concat_sequence  concatenated_sequence         83.471               121   \n",
       "205  concat_sequence  concatenated_sequence         89.873                79   \n",
       "206  concat_sequence  concatenated_sequence         71.128               523   \n",
       "207  concat_sequence  concatenated_sequence         98.039                51   \n",
       "208  concat_sequence  concatenated_sequence         75.796               157   \n",
       "\n",
       "     mismatches  gaps  q_start    q_end  s_start    s_end        evalue  \\\n",
       "0          2458   336   394896   406227   488111   499430  0.000000e+00   \n",
       "1           873    46   994229   999392  2701780  2696619  0.000000e+00   \n",
       "2           887    74   749899   754961  3290594  3295672  0.000000e+00   \n",
       "3          2046   225   151122   159977    94669   103533  0.000000e+00   \n",
       "4           935    85   659559   664286  3106571  3111291  0.000000e+00   \n",
       "..          ...   ...      ...      ...      ...      ...           ...   \n",
       "204          16     4   568589   568707   390401   390519  3.020000e-21   \n",
       "205           5     3   920303   920378   741961   742039  6.550000e-18   \n",
       "206         118    33   477021   477530  1605051  1605553  6.550000e-18   \n",
       "207           1     0   646568   646618   921483   921433  3.940000e-15   \n",
       "208          36     2  1050035  1050190  1172170  1172015  8.530000e-12   \n",
       "\n",
       "     bit_score  qcov  qcovhsp     qlen     slen  \n",
       "0       5437.0    28        1  1240583  3327926  \n",
       "1       4444.0    28        0  1240583  3327926  \n",
       "2       4041.0    28        0  1240583  3327926  \n",
       "3       3781.0    28        1  1240583  3327926  \n",
       "4       3073.0    28        0  1240583  3327926  \n",
       "..         ...   ...      ...      ...      ...  \n",
       "204      110.0    28        0  1240583  3327926  \n",
       "205       99.0    28        0  1240583  3327926  \n",
       "206       99.0    28        0  1240583  3327926  \n",
       "207       89.8    28        0  1240583  3327926  \n",
       "208       78.7    28        0  1240583  3327926  \n",
       "\n",
       "[209 rows x 16 columns]"
      ]
     },
     "execution_count": 72,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import pandas as pd\n",
    "\n",
    "# Define the column names based on the format of the BLAST output.\n",
    "# The default BLAST tabular output (-outfmt 6) has these columns:\n",
    "column_names = [\n",
    "    \"query_id\", \"subject_id\", \"perc_identity\", \"alignment_length\", \"mismatches\",\n",
    "    \"gaps\", \"q_start\", \"q_end\", \"s_start\", \"s_end\", \"evalue\", \"bit_score\", \"qcov\", \"qcovhsp\", \"qlen\", \"slen\"\n",
    "]\n",
    "\n",
    "# Read the BLAST output file into a pandas DataFrame\n",
    "blast_output_file = \"all_new.blast\"\n",
    "all = pd.read_csv(blast_output_file, sep=\"\\t\", header=None, names=column_names)\n",
    "\n",
    "# Display the first few rows of the DataFrame\n",
    "all"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "id": "0350aa35-d662-40df-bd4f-e3d867639491",
   "metadata": {},
   "outputs": [],
   "source": [
    "all_sorted = all.sort_values(by=[\"perc_identity\", \"alignment_length\"], ascending=[False,False])\n",
    "all_sorted = all_sorted.reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "id": "d4e26bc2-e3a5-43b4-8966-03eeb10f1898",
   "metadata": {},
   "outputs": [],
   "source": [
    "mask2 = default_df_sorted != all_sorted"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "id": "0d5f36e4-aec3-4b16-b1e2-ab615b3ca3a1",
   "metadata": {},
   "outputs": [
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       "      <td>114083</td>\n",
       "      <td>114160</td>\n",
       "      <td>508082</td>\n",
       "      <td>508005</td>\n",
       "      <td>7.830000e-33</td>\n",
       "      <td>145.0</td>\n",
       "      <td>27</td>\n",
       "      <td>0</td>\n",
       "      <td>117204</td>\n",
       "      <td>1120828</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>78</td>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>NZ_JAEPPV010000007.1</td>\n",
       "      <td>98.795</td>\n",
       "      <td>83</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>590225</td>\n",
       "      <td>590306</td>\n",
       "      <td>59361</td>\n",
       "      <td>59443</td>\n",
       "      <td>1.200000e-32</td>\n",
       "      <td>147.0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>646567</td>\n",
       "      <td>125019</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>142</td>\n",
       "      <td>AWFD01000002</td>\n",
       "      <td>NZ_JAEPPV010000003.1</td>\n",
       "      <td>98.039</td>\n",
       "      <td>51</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>51</td>\n",
       "      <td>460887</td>\n",
       "      <td>460837</td>\n",
       "      <td>6.100000e-16</td>\n",
       "      <td>89.8</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>191994</td>\n",
       "      <td>460968</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>182</td>\n",
       "      <td>AWFD01000004</td>\n",
       "      <td>NZ_JAEPPV010000004.1</td>\n",
       "      <td>94.505</td>\n",
       "      <td>91</td>\n",
       "      <td>5</td>\n",
       "      <td>0</td>\n",
       "      <td>59501</td>\n",
       "      <td>59591</td>\n",
       "      <td>171942</td>\n",
       "      <td>172032</td>\n",
       "      <td>1.190000e-31</td>\n",
       "      <td>141.0</td>\n",
       "      <td>12</td>\n",
       "      <td>0</td>\n",
       "      <td>137817</td>\n",
       "      <td>239583</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>137</td>\n",
       "      <td>AWFD01000002</td>\n",
       "      <td>NZ_JAEPPV010000005.1</td>\n",
       "      <td>93.443</td>\n",
       "      <td>122</td>\n",
       "      <td>8</td>\n",
       "      <td>0</td>\n",
       "      <td>122392</td>\n",
       "      <td>122513</td>\n",
       "      <td>218470</td>\n",
       "      <td>218591</td>\n",
       "      <td>9.780000e-44</td>\n",
       "      <td>182.0</td>\n",
       "      <td>21</td>\n",
       "      <td>0</td>\n",
       "      <td>191994</td>\n",
       "      <td>236043</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>204</th>\n",
       "      <td>55</td>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>NZ_JAEPPV010000006.1</td>\n",
       "      <td>72.333</td>\n",
       "      <td>900</td>\n",
       "      <td>217</td>\n",
       "      <td>32</td>\n",
       "      <td>24603</td>\n",
       "      <td>25486</td>\n",
       "      <td>39638</td>\n",
       "      <td>40521</td>\n",
       "      <td>6.880000e-65</td>\n",
       "      <td>254.0</td>\n",
       "      <td>7</td>\n",
       "      <td>0</td>\n",
       "      <td>646567</td>\n",
       "      <td>216801</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>205</th>\n",
       "      <td>132</td>\n",
       "      <td>AWFD01000002</td>\n",
       "      <td>NZ_JAEPPV010000005.1</td>\n",
       "      <td>71.229</td>\n",
       "      <td>1505</td>\n",
       "      <td>379</td>\n",
       "      <td>54</td>\n",
       "      <td>122807</td>\n",
       "      <td>124284</td>\n",
       "      <td>218893</td>\n",
       "      <td>220370</td>\n",
       "      <td>9.170000e-89</td>\n",
       "      <td>331.0</td>\n",
       "      <td>21</td>\n",
       "      <td>1</td>\n",
       "      <td>191994</td>\n",
       "      <td>236043</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>206</th>\n",
       "      <td>114</td>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>NZ_JAEPPV010000001.1</td>\n",
       "      <td>71.128</td>\n",
       "      <td>523</td>\n",
       "      <td>118</td>\n",
       "      <td>33</td>\n",
       "      <td>477021</td>\n",
       "      <td>477530</td>\n",
       "      <td>273001</td>\n",
       "      <td>273503</td>\n",
       "      <td>3.410000e-18</td>\n",
       "      <td>99.0</td>\n",
       "      <td>8</td>\n",
       "      <td>0</td>\n",
       "      <td>646567</td>\n",
       "      <td>1120828</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>207</th>\n",
       "      <td>56</td>\n",
       "      <td>AWFD01000001</td>\n",
       "      <td>NZ_JAEPPV010000006.1</td>\n",
       "      <td>70.676</td>\n",
       "      <td>1006</td>\n",
       "      <td>230</td>\n",
       "      <td>65</td>\n",
       "      <td>93256</td>\n",
       "      <td>94242</td>\n",
       "      <td>105620</td>\n",
       "      <td>106579</td>\n",
       "      <td>1.190000e-37</td>\n",
       "      <td>163.0</td>\n",
       "      <td>7</td>\n",
       "      <td>0</td>\n",
       "      <td>646567</td>\n",
       "      <td>216801</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>208</th>\n",
       "      <td>171</td>\n",
       "      <td>AWFD01000004</td>\n",
       "      <td>NZ_JAEPPV010000002.1</td>\n",
       "      <td>69.864</td>\n",
       "      <td>1032</td>\n",
       "      <td>283</td>\n",
       "      <td>28</td>\n",
       "      <td>59631</td>\n",
       "      <td>60648</td>\n",
       "      <td>461983</td>\n",
       "      <td>460966</td>\n",
       "      <td>1.180000e-36</td>\n",
       "      <td>158.0</td>\n",
       "      <td>9</td>\n",
       "      <td>1</td>\n",
       "      <td>137817</td>\n",
       "      <td>639005</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>209 rows × 17 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     index      query_id            subject_id  perc_identity  \\\n",
       "0      207  AWFD01000005  NZ_JAEPPV010000001.1        100.000   \n",
       "1       78  AWFD01000001  NZ_JAEPPV010000007.1         98.795   \n",
       "2      142  AWFD01000002  NZ_JAEPPV010000003.1         98.039   \n",
       "3      182  AWFD01000004  NZ_JAEPPV010000004.1         94.505   \n",
       "4      137  AWFD01000002  NZ_JAEPPV010000005.1         93.443   \n",
       "..     ...           ...                   ...            ...   \n",
       "204     55  AWFD01000001  NZ_JAEPPV010000006.1         72.333   \n",
       "205    132  AWFD01000002  NZ_JAEPPV010000005.1         71.229   \n",
       "206    114  AWFD01000001  NZ_JAEPPV010000001.1         71.128   \n",
       "207     56  AWFD01000001  NZ_JAEPPV010000006.1         70.676   \n",
       "208    171  AWFD01000004  NZ_JAEPPV010000002.1         69.864   \n",
       "\n",
       "     alignment_length  mismatches  gaps  q_start   q_end  s_start   s_end  \\\n",
       "0                  78           0     0   114083  114160   508082  508005   \n",
       "1                  83           0     1   590225  590306    59361   59443   \n",
       "2                  51           1     0        1      51   460887  460837   \n",
       "3                  91           5     0    59501   59591   171942  172032   \n",
       "4                 122           8     0   122392  122513   218470  218591   \n",
       "..                ...         ...   ...      ...     ...      ...     ...   \n",
       "204               900         217    32    24603   25486    39638   40521   \n",
       "205              1505         379    54   122807  124284   218893  220370   \n",
       "206               523         118    33   477021  477530   273001  273503   \n",
       "207              1006         230    65    93256   94242   105620  106579   \n",
       "208              1032         283    28    59631   60648   461983  460966   \n",
       "\n",
       "           evalue  bit_score  qcov  qcovhsp    qlen     slen  \n",
       "0    7.830000e-33      145.0    27        0  117204  1120828  \n",
       "1    1.200000e-32      147.0     2        0  646567   125019  \n",
       "2    6.100000e-16       89.8     1        0  191994   460968  \n",
       "3    1.190000e-31      141.0    12        0  137817   239583  \n",
       "4    9.780000e-44      182.0    21        0  191994   236043  \n",
       "..            ...        ...   ...      ...     ...      ...  \n",
       "204  6.880000e-65      254.0     7        0  646567   216801  \n",
       "205  9.170000e-89      331.0    21        1  191994   236043  \n",
       "206  3.410000e-18       99.0     8        0  646567  1120828  \n",
       "207  1.190000e-37      163.0     7        0  646567   216801  \n",
       "208  1.180000e-36      158.0     9        1  137817   639005  \n",
       "\n",
       "[209 rows x 17 columns]"
      ]
     },
     "execution_count": 75,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "default_df_sorted"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 76,
   "id": "d5bd0fbc-cd85-4f80-9ccc-3e1234f7883e",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>index</th>\n",
       "      <th>query_id</th>\n",
       "      <th>subject_id</th>\n",
       "      <th>perc_identity</th>\n",
       "      <th>alignment_length</th>\n",
       "      <th>mismatches</th>\n",
       "      <th>gaps</th>\n",
       "      <th>q_start</th>\n",
       "      <th>q_end</th>\n",
       "      <th>s_start</th>\n",
       "      <th>s_end</th>\n",
       "      <th>evalue</th>\n",
       "      <th>bit_score</th>\n",
       "      <th>qcov</th>\n",
       "      <th>qcovhsp</th>\n",
       "      <th>qlen</th>\n",
       "      <th>slen</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>196</td>\n",
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       "      <td>concatenated_sequence</td>\n",
       "      <td>100.000</td>\n",
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       "      <td>8.290000e-32</td>\n",
       "      <td>145.0</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>195</td>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>98.795</td>\n",
       "      <td>83</td>\n",
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       "      <td>1</td>\n",
       "      <td>590225</td>\n",
       "      <td>590306</td>\n",
       "      <td>394938</td>\n",
       "      <td>395020</td>\n",
       "      <td>2.310000e-32</td>\n",
       "      <td>147.0</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>207</td>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>98.039</td>\n",
       "      <td>51</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>646568</td>\n",
       "      <td>646618</td>\n",
       "      <td>921483</td>\n",
       "      <td>921433</td>\n",
       "      <td>3.940000e-15</td>\n",
       "      <td>89.8</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>198</td>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>94.505</td>\n",
       "      <td>91</td>\n",
       "      <td>5</td>\n",
       "      <td>0</td>\n",
       "      <td>1045063</td>\n",
       "      <td>1045153</td>\n",
       "      <td>1175939</td>\n",
       "      <td>1176029</td>\n",
       "      <td>1.070000e-30</td>\n",
       "      <td>141.0</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>188</td>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>93.443</td>\n",
       "      <td>122</td>\n",
       "      <td>8</td>\n",
       "      <td>0</td>\n",
       "      <td>768959</td>\n",
       "      <td>769080</td>\n",
       "      <td>3310353</td>\n",
       "      <td>3310474</td>\n",
       "      <td>6.320000e-43</td>\n",
       "      <td>182.0</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>204</th>\n",
       "      <td>176</td>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>72.333</td>\n",
       "      <td>900</td>\n",
       "      <td>217</td>\n",
       "      <td>32</td>\n",
       "      <td>24603</td>\n",
       "      <td>25486</td>\n",
       "      <td>158414</td>\n",
       "      <td>159297</td>\n",
       "      <td>1.320000e-64</td>\n",
       "      <td>254.0</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>205</th>\n",
       "      <td>169</td>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>71.229</td>\n",
       "      <td>1505</td>\n",
       "      <td>379</td>\n",
       "      <td>54</td>\n",
       "      <td>769374</td>\n",
       "      <td>770851</td>\n",
       "      <td>3310776</td>\n",
       "      <td>3312253</td>\n",
       "      <td>5.930000e-88</td>\n",
       "      <td>331.0</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>206</th>\n",
       "      <td>206</td>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>71.128</td>\n",
       "      <td>523</td>\n",
       "      <td>118</td>\n",
       "      <td>33</td>\n",
       "      <td>477021</td>\n",
       "      <td>477530</td>\n",
       "      <td>1605051</td>\n",
       "      <td>1605553</td>\n",
       "      <td>6.550000e-18</td>\n",
       "      <td>99.0</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>207</th>\n",
       "      <td>191</td>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>70.676</td>\n",
       "      <td>1006</td>\n",
       "      <td>230</td>\n",
       "      <td>65</td>\n",
       "      <td>93256</td>\n",
       "      <td>94242</td>\n",
       "      <td>224396</td>\n",
       "      <td>225355</td>\n",
       "      <td>2.290000e-37</td>\n",
       "      <td>163.0</td>\n",
       "      <td>28</td>\n",
       "      <td>0</td>\n",
       "      <td>1240583</td>\n",
       "      <td>3327926</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>208</th>\n",
       "      <td>194</td>\n",
       "      <td>concat_sequence</td>\n",
       "      <td>concatenated_sequence</td>\n",
       "      <td>69.864</td>\n",
       "      <td>1032</td>\n",
       "      <td>283</td>\n",
       "      <td>28</td>\n",
       "      <td>1045193</td>\n",
       "      <td>1046210</td>\n",
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       "     index         query_id             subject_id  perc_identity  \\\n",
       "0      196  concat_sequence  concatenated_sequence        100.000   \n",
       "1      195  concat_sequence  concatenated_sequence         98.795   \n",
       "2      207  concat_sequence  concatenated_sequence         98.039   \n",
       "3      198  concat_sequence  concatenated_sequence         94.505   \n",
       "4      188  concat_sequence  concatenated_sequence         93.443   \n",
       "..     ...              ...                    ...            ...   \n",
       "204    176  concat_sequence  concatenated_sequence         72.333   \n",
       "205    169  concat_sequence  concatenated_sequence         71.229   \n",
       "206    206  concat_sequence  concatenated_sequence         71.128   \n",
       "207    191  concat_sequence  concatenated_sequence         70.676   \n",
       "208    194  concat_sequence  concatenated_sequence         69.864   \n",
       "\n",
       "     alignment_length  mismatches  gaps  q_start    q_end  s_start    s_end  \\\n",
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       "3                  91           5     0  1045063  1045153  1175939  1176029   \n",
       "4                 122           8     0   768959   769080  3310353  3310474   \n",
       "..                ...         ...   ...      ...      ...      ...      ...   \n",
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       "205              1505         379    54   769374   770851  3310776  3312253   \n",
       "206               523         118    33   477021   477530  1605051  1605553   \n",
       "207              1006         230    65    93256    94242   224396   225355   \n",
       "208              1032         283    28  1045193  1046210  2914861  2913844   \n",
       "\n",
       "           evalue  bit_score  qcov  qcovhsp     qlen     slen  \n",
       "0    8.290000e-32      145.0    28        0  1240583  3327926  \n",
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       "4    6.320000e-43      182.0    28        0  1240583  3327926  \n",
       "..            ...        ...   ...      ...      ...      ...  \n",
       "204  1.320000e-64      254.0    28        0  1240583  3327926  \n",
       "205  5.930000e-88      331.0    28        0  1240583  3327926  \n",
       "206  6.550000e-18       99.0    28        0  1240583  3327926  \n",
       "207  2.290000e-37      163.0    28        0  1240583  3327926  \n",
       "208  1.060000e-35      158.0    28        0  1240583  3327926  \n",
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       "      <th>evalue</th>\n",
       "      <th>bit_score</th>\n",
       "      <th>qcov</th>\n",
       "      <th>qcovhsp</th>\n",
       "      <th>qlen</th>\n",
       "      <th>slen</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>65</th>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>82</th>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>149</th>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     index  query_id  subject_id  perc_identity  alignment_length  mismatches  \\\n",
       "65    True      True        True           True              True        True   \n",
       "82    True      True        True           True              True        True   \n",
       "149  False      True        True           True              True        True   \n",
       "\n",
       "     gaps  q_start  q_end  s_start  s_end  evalue  bit_score  qcov  qcovhsp  \\\n",
       "65   True     True   True     True   True   False      False  True     True   \n",
       "82   True    False  False     True   True   False      False  True    False   \n",
       "149  True    False  False     True   True   False      False  True     True   \n",
       "\n",
       "     qlen  slen  \n",
       "65   True  True  \n",
       "82   True  True  \n",
       "149  True  True  "
      ]
     },
     "execution_count": 79,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mask2[mask2['alignment_length']==True]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "id": "dee1f354-f0de-4dbf-8b84-4463133d14d3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "index                                116\n",
       "query_id                    AWFD01000002\n",
       "subject_id          NZ_JAEPPV010000005.1\n",
       "perc_identity                     81.179\n",
       "alignment_length                    5106\n",
       "mismatches                           891\n",
       "gaps                                  70\n",
       "q_start                           103332\n",
       "q_end                             108394\n",
       "s_start                           198711\n",
       "s_end                             203789\n",
       "evalue                               0.0\n",
       "bit_score                         4041.0\n",
       "qcov                                  21\n",
       "qcovhsp                                3\n",
       "qlen                              191994\n",
       "slen                              236043\n",
       "Name: 65, dtype: object"
      ]
     },
     "execution_count": 81,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "default_df_sorted.loc[65]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 82,
   "id": "3021ee0a-7694-4f31-9783-b1ea40a4f5d4",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "index                                   2\n",
       "query_id                  concat_sequence\n",
       "subject_id          concatenated_sequence\n",
       "perc_identity                      81.186\n",
       "alignment_length                     5108\n",
       "mismatches                            887\n",
       "gaps                                   74\n",
       "q_start                            749899\n",
       "q_end                              754961\n",
       "s_start                           3290594\n",
       "s_end                             3295672\n",
       "evalue                                0.0\n",
       "bit_score                          4041.0\n",
       "qcov                                   28\n",
       "qcovhsp                                 0\n",
       "qlen                              1240583\n",
       "slen                              3327926\n",
       "Name: 65, dtype: object"
      ]
     },
     "execution_count": 82,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "all_sorted.loc[65]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 83,
   "id": "7e2fa917-64f4-4a9a-9bbe-c5db7f81b79d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "index                                 83\n",
       "query_id                    AWFD01000001\n",
       "subject_id          NZ_JAEPPV010000001.1\n",
       "perc_identity                     79.899\n",
       "alignment_length                    2378\n",
       "mismatches                           423\n",
       "gaps                                  55\n",
       "q_start                           204143\n",
       "q_end                             206487\n",
       "s_start                            14036\n",
       "s_end                              16391\n",
       "evalue                               0.0\n",
       "bit_score                         1692.0\n",
       "qcov                                   8\n",
       "qcovhsp                                0\n",
       "qlen                              646567\n",
       "slen                             1120828\n",
       "Name: 82, dtype: object"
      ]
     },
     "execution_count": 83,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "default_df_sorted.loc[82]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 84,
   "id": "75298134-64c3-4494-bce8-c96676c2e845",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "index                                  31\n",
       "query_id                  concat_sequence\n",
       "subject_id          concatenated_sequence\n",
       "perc_identity                      79.882\n",
       "alignment_length                     2376\n",
       "mismatches                            427\n",
       "gaps                                   51\n",
       "q_start                            204143\n",
       "q_end                              206487\n",
       "s_start                           1346086\n",
       "s_end                             1348441\n",
       "evalue                                0.0\n",
       "bit_score                          1692.0\n",
       "qcov                                   28\n",
       "qcovhsp                                 0\n",
       "qlen                              1240583\n",
       "slen                              3327926\n",
       "Name: 82, dtype: object"
      ]
     },
     "execution_count": 84,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "all_sorted.loc[82]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 85,
   "id": "48a3c007-aae0-4227-b823-bc930f14c052",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "index                                  0\n",
       "query_id                    AWFD01000001\n",
       "subject_id          NZ_JAEPPV010000003.1\n",
       "perc_identity                      75.69\n",
       "alignment_length                   11493\n",
       "mismatches                          2460\n",
       "gaps                                 334\n",
       "q_start                           394896\n",
       "q_end                             406227\n",
       "s_start                            27515\n",
       "s_end                              38834\n",
       "evalue                               0.0\n",
       "bit_score                         5437.0\n",
       "qcov                                   6\n",
       "qcovhsp                                2\n",
       "qlen                              646567\n",
       "slen                              460968\n",
       "Name: 149, dtype: object"
      ]
     },
     "execution_count": 85,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "default_df_sorted.loc[149]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 86,
   "id": "33b1a719-7fa5-4c2d-814f-bf215acb4d12",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "index                                   0\n",
       "query_id                  concat_sequence\n",
       "subject_id          concatenated_sequence\n",
       "perc_identity                      75.692\n",
       "alignment_length                    11494\n",
       "mismatches                           2458\n",
       "gaps                                  336\n",
       "q_start                            394896\n",
       "q_end                              406227\n",
       "s_start                            488111\n",
       "s_end                              499430\n",
       "evalue                                0.0\n",
       "bit_score                          5437.0\n",
       "qcov                                   28\n",
       "qcovhsp                                 1\n",
       "qlen                              1240583\n",
       "slen                              3327926\n",
       "Name: 149, dtype: object"
      ]
     },
     "execution_count": 86,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "all_sorted.loc[149]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "18dd305f-57f0-40f6-a43f-869dc9821428",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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