genelist2bed.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# blast route"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/opt/anaconda/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:79: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n",
      "/opt/anaconda/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:80: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n",
      "/opt/anaconda/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:83: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n",
      "/opt/anaconda/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:84: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n",
      "/opt/anaconda/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:86: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n"
     ]
    },
    {
     "ename": "NameError",
     "evalue": "name 'flankinging' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-2-9cf933a7218b>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     85\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     86\u001b[0m \u001b[0mresult_values\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'End'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mresult_values\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'End'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mflanking\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 87\u001b[0;31m \u001b[0mbedfile\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfileA\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'_blastp.tbl'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m'_'\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mflankinging\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m'.bed'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     88\u001b[0m \u001b[0mdf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mto_csv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbedfile\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msep\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'\\t'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mindex\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mNameError\u001b[0m: name 'flankinging' is not defined"
     ]
    }
   ],
   "source": [
    "import pandas as pd\n",
    "blast_column_names = [\"qseqid\", \"sseqid\", \"pident\", \"length\", \"mismatch\", \"gapopen\", \"qstart\", \"qend\", \"sstart\", \"send\", \"evalue\", \"bitscore\"]                         \n",
    "gff_file = '/bioinfo/palm/ref/dura/dura_ref.gff'\n",
    "gff_column_names = ['Seqid', 'Source', 'Type', 'Start', 'End', 'Score', 'Strand', 'Phase', 'Attributes']\n",
    "bs = 0 #bitscore filtering\n",
    "n = 3 #hits per gene\n",
    "flanking = 2000 #flanking regions upstream and downstream\n",
    "fileA = 'ABA_dura_blastp.tbl'\n",
    "fileB = 'dura_ABA_blastp.tbl'\n",
    "\n",
    "# Read data from file A\n",
    "fileA_data = pd.read_csv(fileA, sep='\\t', names=blast_column_names)\n",
    "\n",
    "# Read data from file B\n",
    "fileB_data = pd.read_csv(fileB, sep='\\t', names=blast_column_names)\n",
    "\n",
    "# Initialize an empty list to store the results\n",
    "result_pairs = {}\n",
    "\n",
    "# Loop through unique values in 'sseqid' column in file A\n",
    "\n",
    "for sseqid_a in fileA_data['sseqid'].unique():\n",
    "    count = 0\n",
    "    # Filter rows in file A where 'sseqid' is equal to the current value in the loop\n",
    "    filtered_rows = fileA_data[fileA_data['sseqid'] == sseqid_a]\n",
    "    # Sort the filtered rows by 'bitscore' in descending order\n",
    "    sorted_rows = filtered_rows.sort_values(by='bitscore', ascending=False)\n",
    "    # Iterate through the sorted rows\n",
    "    count = 0\n",
    "    for _, max_bitscore_row in sorted_rows.iterrows():\n",
    "        if count < n:\n",
    "            # Get the value for 'qseqid' in the current row\n",
    "            qseqid_b = max_bitscore_row['qseqid']\n",
    "\n",
    "            # Check if the row exists in file B with 'sseqid' == 'b' and 'qseqid' == 'a'\n",
    "            matching_row = fileB_data[(fileB_data['sseqid'] == qseqid_b) & (fileB_data['qseqid'] == sseqid_a)]\n",
    "\n",
    "            # If the matching row exists and 'bitscore' is greater than the threshold, add 'a' and 'b' to the result_pairs dictionary\n",
    "            if not matching_row.empty and max_bitscore_row['bitscore'] > bs:\n",
    "                sseqid_a = sseqid_a.split('-mRNA')[0]\n",
    "                qseqid_b = qseqid_b.split('-mRNA')[0]\n",
    "                if sseqid_a not in result_pairs:\n",
    "                    result_pairs[sseqid_a] = []\n",
    "\n",
    "                result_pairs[sseqid_a].append(qseqid_b)\n",
    "                count += 1\n",
    "    \n",
    "# get the local gene list\n",
    "local_list = []\n",
    "for sseqid_a, qseqid_b_list in result_pairs.items():\n",
    "    local_list += qseqid_b_list\n",
    "            \n",
    "# Now we need to get the position of genes from the gff file.      \n",
    "\n",
    "# Read data from the file\n",
    "df = pd.read_csv(gff_file, sep='\\t',comment='#', names=gff_column_names)\n",
    "# Function to parse the 'Attributes' column in gff file and convert it into a dictionary of key-value pairs\n",
    "def parse_attributes(attribute_str):\n",
    "    attribute_pairs = attribute_str.split(';')\n",
    "    attribute_dict = {}\n",
    "    for pair in attribute_pairs:\n",
    "        if len(pair.split('=')) == 2:\n",
    "            key, value = pair.split('=')\n",
    "        else:\n",
    "            key = pair.split('=')[0]\n",
    "            value = ''\n",
    "        attribute_dict[key] = value\n",
    "    return attribute_dict\n",
    "df1 = df['Attributes'].apply(parse_attributes).apply(pd.Series)\n",
    "file_data = pd.concat([df.drop('Attributes', axis=1), df1], axis=1)\n",
    "\n",
    "# Filter rows where value from column A is in the list\n",
    "filtered_rows = file_data[file_data['ID'].isin(local_list)]\n",
    "\n",
    "# Extract values from column B and C from the filtered rows\n",
    "result_values = filtered_rows[['Seqid', 'Start','End','ID']]\n",
    "\n",
    "# Convert columns A and B to numeric\n",
    "result_values['Start'] = pd.to_numeric(result_values['Start'])\n",
    "result_values['End'] = pd.to_numeric(result_values['End'])\n",
    "\n",
    "# Perform the operations and apply the conditions\n",
    "result_values['Start'] = result_values['Start'] - flanking\n",
    "result_values['Start'] = result_values['Start'].apply(lambda x: max(0, x))  # Set negative values to 0\n",
    "\n",
    "result_values['End'] = result_values['End'] + flanking\n",
    "bedfile = fileA.split('_blastp.tbl')[0] + '_' + str(flanking) + '.bed'\n",
    "result_values.to_csv(bedfile, sep='\\t', index=False)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Seqid</th>\n",
       "      <th>Source</th>\n",
       "      <th>Type</th>\n",
       "      <th>Start</th>\n",
       "      <th>End</th>\n",
       "      <th>Score</th>\n",
       "      <th>Strand</th>\n",
       "      <th>Phase</th>\n",
       "      <th>ID</th>\n",
       "      <th>Name</th>\n",
       "      <th>Alias</th>\n",
       "      <th></th>\n",
       "      <th>Parent</th>\n",
       "      <th>_AED</th>\n",
       "      <th>_QI</th>\n",
       "      <th>_eAED</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>egu.contig.1973</td>\n",
       "      <td>maker</td>\n",
       "      <td>gene</td>\n",
       "      <td>10123</td>\n",
       "      <td>11712</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>Egu032749</td>\n",
       "      <td>Egu032749</td>\n",
       "      <td>snap_masked-egu.contig.1973-processed-gene-0.0</td>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>egu.contig.1973</td>\n",
       "      <td>maker</td>\n",
       "      <td>mRNA</td>\n",
       "      <td>10123</td>\n",
       "      <td>11712</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>Egu032749-mRNA-1</td>\n",
       "      <td>Egu032749-mRNA-1</td>\n",
       "      <td>snap_masked-egu.contig.1973-processed-gene-0.0...</td>\n",
       "      <td></td>\n",
       "      <td>Egu032749</td>\n",
       "      <td>0.06</td>\n",
       "      <td>0|0|0|0.5|1|1|2|0|472</td>\n",
       "      <td>0.04</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>egu.contig.1973</td>\n",
       "      <td>maker</td>\n",
       "      <td>exon</td>\n",
       "      <td>10123</td>\n",
       "      <td>11511</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>Egu032749-mRNA-1:1</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td></td>\n",
       "      <td>Egu032749-mRNA-1</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>egu.contig.1973</td>\n",
       "      <td>maker</td>\n",
       "      <td>exon</td>\n",
       "      <td>11686</td>\n",
       "      <td>11712</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>Egu032749-mRNA-1:2</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td></td>\n",
       "      <td>Egu032749-mRNA-1</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>egu.contig.1973</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>10123</td>\n",
       "      <td>11511</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>0</td>\n",
       "      <td>Egu032749-mRNA-1:cds</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td></td>\n",
       "      <td>Egu032749-mRNA-1</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>egu.contig.1973</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>11686</td>\n",
       "      <td>11712</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>0</td>\n",
       "      <td>Egu032749-mRNA-1:cds</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td></td>\n",
       "      <td>Egu032749-mRNA-1</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>egu.contig.1477</td>\n",
       "      <td>maker</td>\n",
       "      <td>gene</td>\n",
       "      <td>157297</td>\n",
       "      <td>158409</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>Egu032743</td>\n",
       "      <td>Egu032743</td>\n",
       "      <td>maker-egu.contig.1477-snap-gene-0.0</td>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "             Seqid Source  Type   Start     End Score Strand Phase  \\\n",
       "0  egu.contig.1973  maker  gene   10123   11712     .      +     .   \n",
       "1  egu.contig.1973  maker  mRNA   10123   11712     .      +     .   \n",
       "2  egu.contig.1973  maker  exon   10123   11511     .      +     .   \n",
       "3  egu.contig.1973  maker  exon   11686   11712     .      +     .   \n",
       "4  egu.contig.1973  maker   CDS   10123   11511     .      +     0   \n",
       "5  egu.contig.1973  maker   CDS   11686   11712     .      +     0   \n",
       "6  egu.contig.1477  maker  gene  157297  158409     .      +     .   \n",
       "\n",
       "                     ID              Name  \\\n",
       "0             Egu032749         Egu032749   \n",
       "1      Egu032749-mRNA-1  Egu032749-mRNA-1   \n",
       "2    Egu032749-mRNA-1:1               NaN   \n",
       "3    Egu032749-mRNA-1:2               NaN   \n",
       "4  Egu032749-mRNA-1:cds               NaN   \n",
       "5  Egu032749-mRNA-1:cds               NaN   \n",
       "6             Egu032743         Egu032743   \n",
       "\n",
       "                                               Alias              Parent  \\\n",
       "0     snap_masked-egu.contig.1973-processed-gene-0.0                 NaN   \n",
       "1  snap_masked-egu.contig.1973-processed-gene-0.0...           Egu032749   \n",
       "2                                                NaN    Egu032749-mRNA-1   \n",
       "3                                                NaN    Egu032749-mRNA-1   \n",
       "4                                                NaN    Egu032749-mRNA-1   \n",
       "5                                                NaN    Egu032749-mRNA-1   \n",
       "6                maker-egu.contig.1477-snap-gene-0.0                 NaN   \n",
       "\n",
       "   _AED                    _QI _eAED  \n",
       "0   NaN                    NaN   NaN  \n",
       "1  0.06  0|0|0|0.5|1|1|2|0|472  0.04  \n",
       "2   NaN                    NaN   NaN  \n",
       "3   NaN                    NaN   NaN  \n",
       "4   NaN                    NaN   NaN  \n",
       "5   NaN                    NaN   NaN  \n",
       "6   NaN                    NaN   NaN  "
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "df['Attributes'].apply(parse_attributes).apply(pd.Series)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Seqid</th>\n",
       "      <th>Source</th>\n",
       "      <th>Type</th>\n",
       "      <th>Start</th>\n",
       "      <th>End</th>\n",
       "      <th>Score</th>\n",
       "      <th>Strand</th>\n",
       "      <th>Phase</th>\n",
       "      <th>Attributes</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>egu.contig.1973</td>\n",
       "      <td>maker</td>\n",
       "      <td>gene</td>\n",
       "      <td>10123</td>\n",
       "      <td>11712</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032749;Name=Egu032749;Alias=snap_masked-...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>egu.contig.1973</td>\n",
       "      <td>maker</td>\n",
       "      <td>mRNA</td>\n",
       "      <td>10123</td>\n",
       "      <td>11712</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032749-mRNA-1;Parent=Egu032749;Name=Egu0...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>egu.contig.1973</td>\n",
       "      <td>maker</td>\n",
       "      <td>exon</td>\n",
       "      <td>10123</td>\n",
       "      <td>11511</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032749-mRNA-1:1;Parent=Egu032749-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>egu.contig.1973</td>\n",
       "      <td>maker</td>\n",
       "      <td>exon</td>\n",
       "      <td>11686</td>\n",
       "      <td>11712</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032749-mRNA-1:2;Parent=Egu032749-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>egu.contig.1973</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>10123</td>\n",
       "      <td>11511</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>0</td>\n",
       "      <td>ID=Egu032749-mRNA-1:cds;Parent=Egu032749-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>egu.contig.1973</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>11686</td>\n",
       "      <td>11712</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>0</td>\n",
       "      <td>ID=Egu032749-mRNA-1:cds;Parent=Egu032749-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>egu.contig.1477</td>\n",
       "      <td>maker</td>\n",
       "      <td>gene</td>\n",
       "      <td>157297</td>\n",
       "      <td>158409</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032743;Name=Egu032743;Alias=maker-egu.co...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>egu.contig.1477</td>\n",
       "      <td>maker</td>\n",
       "      <td>mRNA</td>\n",
       "      <td>157297</td>\n",
       "      <td>158409</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032743-mRNA-1;Parent=Egu032743;Name=Egu0...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>egu.contig.1477</td>\n",
       "      <td>maker</td>\n",
       "      <td>exon</td>\n",
       "      <td>157297</td>\n",
       "      <td>157322</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032743-mRNA-1:1;Parent=Egu032743-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>egu.contig.1477</td>\n",
       "      <td>maker</td>\n",
       "      <td>exon</td>\n",
       "      <td>157819</td>\n",
       "      <td>158409</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032743-mRNA-1:2;Parent=Egu032743-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>egu.contig.1477</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>157297</td>\n",
       "      <td>157322</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>0</td>\n",
       "      <td>ID=Egu032743-mRNA-1:cds;Parent=Egu032743-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>egu.contig.1477</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>157819</td>\n",
       "      <td>158161</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>1</td>\n",
       "      <td>ID=Egu032743-mRNA-1:cds;Parent=Egu032743-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>egu.contig.1477</td>\n",
       "      <td>maker</td>\n",
       "      <td>three_prime_UTR</td>\n",
       "      <td>158162</td>\n",
       "      <td>158409</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032743-mRNA-1:three_prime_utr;Parent=Egu...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>egu.contig.1784</td>\n",
       "      <td>maker</td>\n",
       "      <td>gene</td>\n",
       "      <td>3465</td>\n",
       "      <td>4615</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032692;Name=Egu032692;Alias=maker-egu.co...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>egu.contig.1784</td>\n",
       "      <td>maker</td>\n",
       "      <td>mRNA</td>\n",
       "      <td>3465</td>\n",
       "      <td>4615</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032692-mRNA-1;Parent=Egu032692;Name=Egu0...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>egu.contig.1784</td>\n",
       "      <td>maker</td>\n",
       "      <td>exon</td>\n",
       "      <td>3465</td>\n",
       "      <td>3606</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032692-mRNA-1:2;Parent=Egu032692-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>egu.contig.1784</td>\n",
       "      <td>maker</td>\n",
       "      <td>exon</td>\n",
       "      <td>4209</td>\n",
       "      <td>4615</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032692-mRNA-1:1;Parent=Egu032692-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>egu.contig.1784</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>4209</td>\n",
       "      <td>4615</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>0</td>\n",
       "      <td>ID=Egu032692-mRNA-1:cds;Parent=Egu032692-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>egu.contig.1784</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>3465</td>\n",
       "      <td>3606</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>1</td>\n",
       "      <td>ID=Egu032692-mRNA-1:cds;Parent=Egu032692-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>egu.contig.1784</td>\n",
       "      <td>maker</td>\n",
       "      <td>gene</td>\n",
       "      <td>20510</td>\n",
       "      <td>56429</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032693;Name=Egu032693;Alias=maker-egu.co...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>egu.contig.1784</td>\n",
       "      <td>maker</td>\n",
       "      <td>mRNA</td>\n",
       "      <td>20510</td>\n",
       "      <td>56429</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032693-mRNA-1;Parent=Egu032693;Name=Egu0...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>egu.contig.1784</td>\n",
       "      <td>maker</td>\n",
       "      <td>exon</td>\n",
       "      <td>20510</td>\n",
       "      <td>20542</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032693-mRNA-1:2;Parent=Egu032693-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>egu.contig.1784</td>\n",
       "      <td>maker</td>\n",
       "      <td>exon</td>\n",
       "      <td>56019</td>\n",
       "      <td>56429</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032693-mRNA-1:1;Parent=Egu032693-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>egu.contig.1784</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>56019</td>\n",
       "      <td>56429</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>0</td>\n",
       "      <td>ID=Egu032693-mRNA-1:cds;Parent=Egu032693-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>egu.contig.1784</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>20510</td>\n",
       "      <td>20542</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>0</td>\n",
       "      <td>ID=Egu032693-mRNA-1:cds;Parent=Egu032693-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>egu.contig.1415</td>\n",
       "      <td>maker</td>\n",
       "      <td>gene</td>\n",
       "      <td>82686</td>\n",
       "      <td>84008</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032775;Name=Egu032775;Alias=snap_masked-...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>egu.contig.1415</td>\n",
       "      <td>maker</td>\n",
       "      <td>mRNA</td>\n",
       "      <td>82686</td>\n",
       "      <td>84008</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032775-mRNA-1;Parent=Egu032775;Name=Egu0...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>egu.contig.1415</td>\n",
       "      <td>maker</td>\n",
       "      <td>exon</td>\n",
       "      <td>82686</td>\n",
       "      <td>84008</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032775-mRNA-1:1;Parent=Egu032775-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>egu.contig.1415</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>82686</td>\n",
       "      <td>84008</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>0</td>\n",
       "      <td>ID=Egu032775-mRNA-1:cds;Parent=Egu032775-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>egu.contig.1962</td>\n",
       "      <td>maker</td>\n",
       "      <td>gene</td>\n",
       "      <td>13973</td>\n",
       "      <td>23401</td>\n",
       "      <td>.</td>\n",
       "      <td>+</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032522;Name=Egu032522;Alias=snap_masked-...</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615957</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>289762</td>\n",
       "      <td>289833</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>1</td>\n",
       "      <td>ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615958</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>289557</td>\n",
       "      <td>289637</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>1</td>\n",
       "      <td>ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615959</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>289238</td>\n",
       "      <td>289422</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>1</td>\n",
       "      <td>ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615960</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>281941</td>\n",
       "      <td>282218</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>2</td>\n",
       "      <td>ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615961</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>281718</td>\n",
       "      <td>281844</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>0</td>\n",
       "      <td>ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615962</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>280181</td>\n",
       "      <td>280249</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>2</td>\n",
       "      <td>ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615963</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>279893</td>\n",
       "      <td>280085</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>2</td>\n",
       "      <td>ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615964</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>278640</td>\n",
       "      <td>279072</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>1</td>\n",
       "      <td>ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615965</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>three_prime_UTR</td>\n",
       "      <td>278427</td>\n",
       "      <td>278639</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032211-mRNA-1:three_prime_utr;Parent=Egu...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615966</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>five_prime_UTR</td>\n",
       "      <td>293033</td>\n",
       "      <td>293321</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032211-mRNA-4:five_prime_utr;Parent=Egu0...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615967</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>292672</td>\n",
       "      <td>293032</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>0</td>\n",
       "      <td>ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615968</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>291902</td>\n",
       "      <td>292037</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>2</td>\n",
       "      <td>ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615969</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>291744</td>\n",
       "      <td>291815</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>1</td>\n",
       "      <td>ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615970</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>289762</td>\n",
       "      <td>289833</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>1</td>\n",
       "      <td>ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615971</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>289557</td>\n",
       "      <td>289637</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>1</td>\n",
       "      <td>ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615972</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>289238</td>\n",
       "      <td>289422</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>1</td>\n",
       "      <td>ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615973</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>280181</td>\n",
       "      <td>280249</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>2</td>\n",
       "      <td>ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615974</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>279893</td>\n",
       "      <td>280085</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>2</td>\n",
       "      <td>ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615975</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>278640</td>\n",
       "      <td>279072</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>1</td>\n",
       "      <td>ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615976</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>three_prime_UTR</td>\n",
       "      <td>278427</td>\n",
       "      <td>278639</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032211-mRNA-4:three_prime_utr;Parent=Egu...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615977</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>five_prime_UTR</td>\n",
       "      <td>293033</td>\n",
       "      <td>293321</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032211-mRNA-2:five_prime_utr;Parent=Egu0...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615978</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>292672</td>\n",
       "      <td>293032</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>0</td>\n",
       "      <td>ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615979</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>282873</td>\n",
       "      <td>283120</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>2</td>\n",
       "      <td>ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615980</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>282165</td>\n",
       "      <td>282236</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>0</td>\n",
       "      <td>ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615981</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>281941</td>\n",
       "      <td>282138</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>0</td>\n",
       "      <td>ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615982</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>281718</td>\n",
       "      <td>281844</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>0</td>\n",
       "      <td>ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615983</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>280181</td>\n",
       "      <td>280249</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>2</td>\n",
       "      <td>ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615984</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>279893</td>\n",
       "      <td>280085</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>2</td>\n",
       "      <td>ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615985</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>CDS</td>\n",
       "      <td>278640</td>\n",
       "      <td>279072</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>1</td>\n",
       "      <td>ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>615986</th>\n",
       "      <td>egu.contig.1149</td>\n",
       "      <td>maker</td>\n",
       "      <td>three_prime_UTR</td>\n",
       "      <td>278427</td>\n",
       "      <td>278639</td>\n",
       "      <td>.</td>\n",
       "      <td>-</td>\n",
       "      <td>.</td>\n",
       "      <td>ID=Egu032211-mRNA-2:three_prime_utr;Parent=Egu...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>615987 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                  Seqid Source             Type   Start     End Score Strand  \\\n",
       "0       egu.contig.1973  maker             gene   10123   11712     .      +   \n",
       "1       egu.contig.1973  maker             mRNA   10123   11712     .      +   \n",
       "2       egu.contig.1973  maker             exon   10123   11511     .      +   \n",
       "3       egu.contig.1973  maker             exon   11686   11712     .      +   \n",
       "4       egu.contig.1973  maker              CDS   10123   11511     .      +   \n",
       "5       egu.contig.1973  maker              CDS   11686   11712     .      +   \n",
       "6       egu.contig.1477  maker             gene  157297  158409     .      +   \n",
       "7       egu.contig.1477  maker             mRNA  157297  158409     .      +   \n",
       "8       egu.contig.1477  maker             exon  157297  157322     .      +   \n",
       "9       egu.contig.1477  maker             exon  157819  158409     .      +   \n",
       "10      egu.contig.1477  maker              CDS  157297  157322     .      +   \n",
       "11      egu.contig.1477  maker              CDS  157819  158161     .      +   \n",
       "12      egu.contig.1477  maker  three_prime_UTR  158162  158409     .      +   \n",
       "13      egu.contig.1784  maker             gene    3465    4615     .      -   \n",
       "14      egu.contig.1784  maker             mRNA    3465    4615     .      -   \n",
       "15      egu.contig.1784  maker             exon    3465    3606     .      -   \n",
       "16      egu.contig.1784  maker             exon    4209    4615     .      -   \n",
       "17      egu.contig.1784  maker              CDS    4209    4615     .      -   \n",
       "18      egu.contig.1784  maker              CDS    3465    3606     .      -   \n",
       "19      egu.contig.1784  maker             gene   20510   56429     .      -   \n",
       "20      egu.contig.1784  maker             mRNA   20510   56429     .      -   \n",
       "21      egu.contig.1784  maker             exon   20510   20542     .      -   \n",
       "22      egu.contig.1784  maker             exon   56019   56429     .      -   \n",
       "23      egu.contig.1784  maker              CDS   56019   56429     .      -   \n",
       "24      egu.contig.1784  maker              CDS   20510   20542     .      -   \n",
       "25      egu.contig.1415  maker             gene   82686   84008     .      -   \n",
       "26      egu.contig.1415  maker             mRNA   82686   84008     .      -   \n",
       "27      egu.contig.1415  maker             exon   82686   84008     .      -   \n",
       "28      egu.contig.1415  maker              CDS   82686   84008     .      -   \n",
       "29      egu.contig.1962  maker             gene   13973   23401     .      +   \n",
       "...                 ...    ...              ...     ...     ...   ...    ...   \n",
       "615957  egu.contig.1149  maker              CDS  289762  289833     .      -   \n",
       "615958  egu.contig.1149  maker              CDS  289557  289637     .      -   \n",
       "615959  egu.contig.1149  maker              CDS  289238  289422     .      -   \n",
       "615960  egu.contig.1149  maker              CDS  281941  282218     .      -   \n",
       "615961  egu.contig.1149  maker              CDS  281718  281844     .      -   \n",
       "615962  egu.contig.1149  maker              CDS  280181  280249     .      -   \n",
       "615963  egu.contig.1149  maker              CDS  279893  280085     .      -   \n",
       "615964  egu.contig.1149  maker              CDS  278640  279072     .      -   \n",
       "615965  egu.contig.1149  maker  three_prime_UTR  278427  278639     .      -   \n",
       "615966  egu.contig.1149  maker   five_prime_UTR  293033  293321     .      -   \n",
       "615967  egu.contig.1149  maker              CDS  292672  293032     .      -   \n",
       "615968  egu.contig.1149  maker              CDS  291902  292037     .      -   \n",
       "615969  egu.contig.1149  maker              CDS  291744  291815     .      -   \n",
       "615970  egu.contig.1149  maker              CDS  289762  289833     .      -   \n",
       "615971  egu.contig.1149  maker              CDS  289557  289637     .      -   \n",
       "615972  egu.contig.1149  maker              CDS  289238  289422     .      -   \n",
       "615973  egu.contig.1149  maker              CDS  280181  280249     .      -   \n",
       "615974  egu.contig.1149  maker              CDS  279893  280085     .      -   \n",
       "615975  egu.contig.1149  maker              CDS  278640  279072     .      -   \n",
       "615976  egu.contig.1149  maker  three_prime_UTR  278427  278639     .      -   \n",
       "615977  egu.contig.1149  maker   five_prime_UTR  293033  293321     .      -   \n",
       "615978  egu.contig.1149  maker              CDS  292672  293032     .      -   \n",
       "615979  egu.contig.1149  maker              CDS  282873  283120     .      -   \n",
       "615980  egu.contig.1149  maker              CDS  282165  282236     .      -   \n",
       "615981  egu.contig.1149  maker              CDS  281941  282138     .      -   \n",
       "615982  egu.contig.1149  maker              CDS  281718  281844     .      -   \n",
       "615983  egu.contig.1149  maker              CDS  280181  280249     .      -   \n",
       "615984  egu.contig.1149  maker              CDS  279893  280085     .      -   \n",
       "615985  egu.contig.1149  maker              CDS  278640  279072     .      -   \n",
       "615986  egu.contig.1149  maker  three_prime_UTR  278427  278639     .      -   \n",
       "\n",
       "       Phase                                         Attributes  \n",
       "0          .  ID=Egu032749;Name=Egu032749;Alias=snap_masked-...  \n",
       "1          .  ID=Egu032749-mRNA-1;Parent=Egu032749;Name=Egu0...  \n",
       "2          .     ID=Egu032749-mRNA-1:1;Parent=Egu032749-mRNA-1;  \n",
       "3          .     ID=Egu032749-mRNA-1:2;Parent=Egu032749-mRNA-1;  \n",
       "4          0   ID=Egu032749-mRNA-1:cds;Parent=Egu032749-mRNA-1;  \n",
       "5          0   ID=Egu032749-mRNA-1:cds;Parent=Egu032749-mRNA-1;  \n",
       "6          .  ID=Egu032743;Name=Egu032743;Alias=maker-egu.co...  \n",
       "7          .  ID=Egu032743-mRNA-1;Parent=Egu032743;Name=Egu0...  \n",
       "8          .     ID=Egu032743-mRNA-1:1;Parent=Egu032743-mRNA-1;  \n",
       "9          .     ID=Egu032743-mRNA-1:2;Parent=Egu032743-mRNA-1;  \n",
       "10         0   ID=Egu032743-mRNA-1:cds;Parent=Egu032743-mRNA-1;  \n",
       "11         1   ID=Egu032743-mRNA-1:cds;Parent=Egu032743-mRNA-1;  \n",
       "12         .  ID=Egu032743-mRNA-1:three_prime_utr;Parent=Egu...  \n",
       "13         .  ID=Egu032692;Name=Egu032692;Alias=maker-egu.co...  \n",
       "14         .  ID=Egu032692-mRNA-1;Parent=Egu032692;Name=Egu0...  \n",
       "15         .     ID=Egu032692-mRNA-1:2;Parent=Egu032692-mRNA-1;  \n",
       "16         .     ID=Egu032692-mRNA-1:1;Parent=Egu032692-mRNA-1;  \n",
       "17         0   ID=Egu032692-mRNA-1:cds;Parent=Egu032692-mRNA-1;  \n",
       "18         1   ID=Egu032692-mRNA-1:cds;Parent=Egu032692-mRNA-1;  \n",
       "19         .  ID=Egu032693;Name=Egu032693;Alias=maker-egu.co...  \n",
       "20         .  ID=Egu032693-mRNA-1;Parent=Egu032693;Name=Egu0...  \n",
       "21         .     ID=Egu032693-mRNA-1:2;Parent=Egu032693-mRNA-1;  \n",
       "22         .     ID=Egu032693-mRNA-1:1;Parent=Egu032693-mRNA-1;  \n",
       "23         0   ID=Egu032693-mRNA-1:cds;Parent=Egu032693-mRNA-1;  \n",
       "24         0   ID=Egu032693-mRNA-1:cds;Parent=Egu032693-mRNA-1;  \n",
       "25         .  ID=Egu032775;Name=Egu032775;Alias=snap_masked-...  \n",
       "26         .  ID=Egu032775-mRNA-1;Parent=Egu032775;Name=Egu0...  \n",
       "27         .     ID=Egu032775-mRNA-1:1;Parent=Egu032775-mRNA-1;  \n",
       "28         0   ID=Egu032775-mRNA-1:cds;Parent=Egu032775-mRNA-1;  \n",
       "29         .  ID=Egu032522;Name=Egu032522;Alias=snap_masked-...  \n",
       "...      ...                                                ...  \n",
       "615957     1   ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;  \n",
       "615958     1   ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;  \n",
       "615959     1   ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;  \n",
       "615960     2   ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;  \n",
       "615961     0   ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;  \n",
       "615962     2   ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;  \n",
       "615963     2   ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;  \n",
       "615964     1   ID=Egu032211-mRNA-1:cds;Parent=Egu032211-mRNA-1;  \n",
       "615965     .  ID=Egu032211-mRNA-1:three_prime_utr;Parent=Egu...  \n",
       "615966     .  ID=Egu032211-mRNA-4:five_prime_utr;Parent=Egu0...  \n",
       "615967     0   ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;  \n",
       "615968     2   ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;  \n",
       "615969     1   ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;  \n",
       "615970     1   ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;  \n",
       "615971     1   ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;  \n",
       "615972     1   ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;  \n",
       "615973     2   ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;  \n",
       "615974     2   ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;  \n",
       "615975     1   ID=Egu032211-mRNA-4:cds;Parent=Egu032211-mRNA-4;  \n",
       "615976     .  ID=Egu032211-mRNA-4:three_prime_utr;Parent=Egu...  \n",
       "615977     .  ID=Egu032211-mRNA-2:five_prime_utr;Parent=Egu0...  \n",
       "615978     0   ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;  \n",
       "615979     2   ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;  \n",
       "615980     0   ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;  \n",
       "615981     0   ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;  \n",
       "615982     0   ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;  \n",
       "615983     2   ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;  \n",
       "615984     2   ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;  \n",
       "615985     1   ID=Egu032211-mRNA-2:cds;Parent=Egu032211-mRNA-2;  \n",
       "615986     .  ID=Egu032211-mRNA-2:three_prime_utr;Parent=Egu...  \n",
       "\n",
       "[615987 rows x 9 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "file_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.9"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}