metadata.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from datetime import datetime, timedelta\n",
    "import os\n",
    "import random\n",
    "import numpy as np\n",
    "import datetime as dt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# sample_ids = []\n",
    "# with open('matt.txt', 'r') as input_f:\n",
    "#     lines = input_f.readlines()\n",
    "#     for line in lines:\n",
    "#         sample_ids.append(line.strip())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Non TX Clinical Sample"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "non_tx_metadata = pd.read_csv('meta_non_tx.tsv', sep='\\t', low_memory=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "non_tx_metadata = non_tx_metadata.fillna('None')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "non_tx_metadata = non_tx_metadata[(non_tx_metadata['Region'] != 'Texas') & ~((non_tx_metadata['Country'] == 'USA') & (non_tx_metadata['Region'] == 'None'))]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "non_tx_metadata = non_tx_metadata[(non_tx_metadata['Country'] == 'USA')]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "# with open(\"us_sampled_sra.txt\", \"w\") as output_f:\n",
    "#     for sra_id in non_tx_metadata['AccessionId'].to_list():\n",
    "#         output_f.write(f\"{sra_id}\\n\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [],
   "source": [
    "# non_tx_metadata.to_csv('metadata_non_tx.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "metadata": {},
   "outputs": [],
   "source": [
    "filtered_metadata = non_tx_metadata.copy()\n",
    "filtered_metadata['Collection_Date'] = pd.to_datetime(filtered_metadata['Collected'], format='%m/%d/%Y')\n",
    "filtered_metadata\n",
    "\n",
    "start = filtered_metadata['Collection_Date'].min()\n",
    "end = start\n",
    "\n",
    "week_offset = dt.timedelta(days = 7)\n",
    "sample_counts = []\n",
    "x_ticklabels = []\n",
    "while end <= filtered_metadata['Collection_Date'].max():\n",
    "    #print(start, end)\n",
    "    end = start + week_offset\n",
    "    \n",
    "    weekly_clinical_df = filtered_metadata[(filtered_metadata['Collection_Date'] >= start) & (filtered_metadata['Collection_Date'] < end)]\n",
    "    weekly_sample_count = weekly_clinical_df.shape[0]\n",
    "    \n",
    "    x_ticklabels.append((start).strftime('%m-%d-%y'))\n",
    "    sample_counts.append(weekly_sample_count)\n",
    "    start = end\n",
    "    \n",
    "x_ticklabels.append((end).strftime('%m-%d-%y'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Text(0.5, 1.0, 'Clinical Sample Count')"
      ]
     },
     "execution_count": 67,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "\n",
    "fontsize = 14\n",
    "fig, ax  = plt.subplots(1, 1, figsize=(6, 4), sharex=True, constrained_layout=True)\n",
    "\n",
    "x = np.arange(len(sample_counts))\n",
    "\n",
    "ax.bar(x, sample_counts, color='black', alpha=1, width=0.8)\n",
    "\n",
    "ax.set_ylim(0,2000)\n",
    "ax.set_xlim(-0.5,len(sample_counts)-0.5)\n",
    "ax.set_xticks(np.arange(len(sample_counts)+1)-0.5)\n",
    "ax.set_xticklabels(x_ticklabels, rotation=90, fontsize=12)\n",
    "\n",
    "ax.set_title('Clinical Sample Count')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "metadata": {},
   "outputs": [],
   "source": [
    "region_df = pd.DataFrame(pd.pivot_table(non_tx_metadata, values='Repository', index='Region', aggfunc='count'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {},
   "outputs": [],
   "source": [
    "region_df = region_df.rename({'Repository': 'Count'}, axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "199"
      ]
     },
     "execution_count": 80,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "other_count = region_df['Count'].sum() - region_df[region_df['Count'] >= 70]['Count'].sum()\n",
    "other_count"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "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>Count</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Region</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>California</th>\n",
       "      <td>2808</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Colorado</th>\n",
       "      <td>2067</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Georgia</th>\n",
       "      <td>169</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Maryland</th>\n",
       "      <td>285</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Massachusetts</th>\n",
       "      <td>893</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>New Jersey</th>\n",
       "      <td>131</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>New Mexico</th>\n",
       "      <td>646</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>New York</th>\n",
       "      <td>182</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>North Carolina</th>\n",
       "      <td>94</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Pennsylvania</th>\n",
       "      <td>258</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Rhode Island</th>\n",
       "      <td>70</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Utah</th>\n",
       "      <td>1167</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                Count\n",
       "Region               \n",
       "California       2808\n",
       "Colorado         2067\n",
       "Georgia           169\n",
       "Maryland          285\n",
       "Massachusetts     893\n",
       "New Jersey        131\n",
       "New Mexico        646\n",
       "New York          182\n",
       "North Carolina     94\n",
       "Pennsylvania      258\n",
       "Rhode Island       70\n",
       "Utah             1167"
      ]
     },
     "execution_count": 81,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "region_df[region_df['Count'] >= 70]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 94,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[2808, 2067, 169, 285, 893, 131, 646, 182, 94, 258, 70, 1167, 199]"
      ]
     },
     "execution_count": 94,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "region_df[region_df['Count'] >= 70]['Count'].to_list() + [other_count]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 97,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['California',\n",
       " 'Colorado',\n",
       " 'Georgia',\n",
       " 'Maryland',\n",
       " 'Massachusetts',\n",
       " 'New Jersey',\n",
       " 'New Mexico',\n",
       " 'New York',\n",
       " 'North Carolina',\n",
       " 'Pennsylvania',\n",
       " 'Rhode Island',\n",
       " 'Utah',\n",
       " 'Others']"
      ]
     },
     "execution_count": 97,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "selected_region_df.index.to_list() + ['Others']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 100,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[Text(0, 0, 'California'),\n",
       " Text(1, 0, 'Colorado'),\n",
       " Text(2, 0, 'Georgia'),\n",
       " Text(3, 0, 'Maryland'),\n",
       " Text(4, 0, 'Massachusetts'),\n",
       " Text(5, 0, 'New Jersey'),\n",
       " Text(6, 0, 'New Mexico'),\n",
       " Text(7, 0, 'New York'),\n",
       " Text(8, 0, 'North Carolina'),\n",
       " Text(9, 0, 'Pennsylvania'),\n",
       " Text(10, 0, 'Rhode Island'),\n",
       " Text(11, 0, 'Utah'),\n",
       " Text(12, 0, 'Other 24 States')]"
      ]
     },
     "execution_count": 100,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "fontsize = 14\n",
    "fig, ax  = plt.subplots(1, 1, figsize=(6, 4), sharex=True, constrained_layout=True)\n",
    "\n",
    "selected_region_df = region_df[region_df['Count'] >= 70]\n",
    "x = np.arange(selected_region_df.shape[0] + 1)\n",
    "\n",
    "sample_counts = selected_region_df['Count'].to_list() + [other_count]\n",
    "x_ticklabels = selected_region_df.index.to_list() + [f'Other {36-12} States']\n",
    "ax.bar(x, sample_counts, color='black', alpha=1, width=0.8)\n",
    "\n",
    "ax.set_xlim(-0.5,len(sample_counts)-0.5)\n",
    "ax.set_xticks(np.arange(len(sample_counts)))\n",
    "ax.set_xticklabels(x_ticklabels, rotation=90, fontsize=12)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [],
   "source": [
    "# for idx, sample_id in enumerate(non_tx_metadata['AccessionId'].to_list()):\n",
    "#     with open(os.path.join(f\"/home/Users/yl181/cdc_harvest_variants/Proposed_Pipeline_SRA_Inputs_Quarc\", f\"hv_job_{idx}.in\"), \"w\") as array_out:\n",
    "#         array_out.write(sample_id)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Texas Clinical Samples"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "metadata = pd.read_csv('PRJNA764181.SraRunTable.txt', low_memory=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['Run', 'Assay Type', 'AvgSpotLen', 'Bases', 'BioProject', 'BioSample',\n",
       "       'BioSampleModel', 'Bytes', 'Center Name', 'Collection_Date', 'Consent',\n",
       "       'DATASTORE filetype', 'DATASTORE provider', 'DATASTORE region',\n",
       "       'dehosting_method (run)', 'Experiment', 'geo_loc_name_country',\n",
       "       'geo_loc_name_country_continent', 'geo_loc_name', 'GISAID_virus_name',\n",
       "       'Host_disease', 'HOST', 'Instrument', 'Isolate', 'Isolation_source',\n",
       "       'Library Name', 'LibraryLayout', 'LibrarySelection', 'LibrarySource',\n",
       "       'Organism', 'Platform', 'purpose_of_sequencing',\n",
       "       'raw_sequence_data_processing_method (run)', 'ReleaseDate',\n",
       "       'create_date', 'version', 'Sample Name', 'SRA Study', 'collected_by',\n",
       "       'Host_age', 'amplicon__PCR_primer_scheme (run)', 'host_sex'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "metadata.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "metadata = metadata.set_index('Run')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "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>Assay Type</th>\n",
       "      <th>AvgSpotLen</th>\n",
       "      <th>Bases</th>\n",
       "      <th>BioProject</th>\n",
       "      <th>BioSample</th>\n",
       "      <th>BioSampleModel</th>\n",
       "      <th>Bytes</th>\n",
       "      <th>Center Name</th>\n",
       "      <th>Collection_Date</th>\n",
       "      <th>Consent</th>\n",
       "      <th>...</th>\n",
       "      <th>raw_sequence_data_processing_method (run)</th>\n",
       "      <th>ReleaseDate</th>\n",
       "      <th>create_date</th>\n",
       "      <th>version</th>\n",
       "      <th>Sample Name</th>\n",
       "      <th>SRA Study</th>\n",
       "      <th>collected_by</th>\n",
       "      <th>Host_age</th>\n",
       "      <th>amplicon__PCR_primer_scheme (run)</th>\n",
       "      <th>host_sex</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Run</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>SRR16040414</th>\n",
       "      <td>WGS</td>\n",
       "      <td>152</td>\n",
       "      <td>123142344</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN21593958</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>43635441</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-08-23</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-09-24T00:00:00Z</td>\n",
       "      <td>2022-04-20T23:59:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-210902C2794</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>TSU - 3100 CLEBURNE ST.</td>\n",
       "      <td>18.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>male</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR16040415</th>\n",
       "      <td>WGS</td>\n",
       "      <td>146</td>\n",
       "      <td>157571814</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN21594074</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>62921122</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-08-11</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-09-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:00:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2109027874</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>SOUTHWEST MSC- 6400 HIGH STAR DRIVE</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>male</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR16040416</th>\n",
       "      <td>WGS</td>\n",
       "      <td>146</td>\n",
       "      <td>317852471</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN21594073</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>128538693</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-08-11</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-09-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:00:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2109027848</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>SOUTHWEST MSC- 6400 HIGH STAR DRIVE</td>\n",
       "      <td>12.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR16040417</th>\n",
       "      <td>WGS</td>\n",
       "      <td>146</td>\n",
       "      <td>534617403</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN21594072</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>220484561</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-08-11</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-09-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:01:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2109027835</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>SOUTHWEST MSC- 6400 HIGH STAR DRIVE</td>\n",
       "      <td>48.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR16040418</th>\n",
       "      <td>WGS</td>\n",
       "      <td>146</td>\n",
       "      <td>190807225</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN21594071</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>79077884</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-08-11</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-09-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:00:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2109027827</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>SOUTHWEST MSC- 6400 HIGH STAR DRIVE</td>\n",
       "      <td>30.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR23686722</th>\n",
       "      <td>WGS</td>\n",
       "      <td>148</td>\n",
       "      <td>120274420</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN33567412</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>42683526</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2023-01-31</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2023-03-02T00:00:00Z</td>\n",
       "      <td>2023-03-02T15:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-23020154868</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>MAGNOLIA HEALTH CENTER - 7037 CAPITOL</td>\n",
       "      <td>40.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>male</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR23686724</th>\n",
       "      <td>WGS</td>\n",
       "      <td>152</td>\n",
       "      <td>136342632</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN33567393</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>66649758</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2023-01-25</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2023-03-02T00:00:00Z</td>\n",
       "      <td>2023-03-02T15:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2302021821</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>MAGNOLIA HEALTH CENTER - 7037 CAPITOL</td>\n",
       "      <td>35.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR23686726</th>\n",
       "      <td>WGS</td>\n",
       "      <td>148</td>\n",
       "      <td>146166280</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN33567409</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>51732494</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2023-01-31</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2023-03-02T00:00:00Z</td>\n",
       "      <td>2023-03-02T15:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-23020154860</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>MAGNOLIA HEALTH CENTER - 7037 CAPITOL</td>\n",
       "      <td>22.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR23686727</th>\n",
       "      <td>WGS</td>\n",
       "      <td>152</td>\n",
       "      <td>207481824</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN33567408</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>104162583</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2023-01-29</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2023-03-02T00:00:00Z</td>\n",
       "      <td>2023-03-02T15:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2302024358</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>HCO INST FORENSIC SCI - 1861 OLD SPANISH TRAIL</td>\n",
       "      <td>71.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>male</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR23686731</th>\n",
       "      <td>WGS</td>\n",
       "      <td>152</td>\n",
       "      <td>181081552</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN33567404</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>88330064</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2023-01-28</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2023-03-02T00:00:00Z</td>\n",
       "      <td>2023-03-02T15:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2302023836</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>SOUTHWEST MSC- 6400 HIGH STAR DRIVE</td>\n",
       "      <td>20.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>10111 rows × 41 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            Assay Type  AvgSpotLen      Bases   BioProject     BioSample  \\\n",
       "Run                                                                        \n",
       "SRR16040414        WGS         152  123142344  PRJNA764181  SAMN21593958   \n",
       "SRR16040415        WGS         146  157571814  PRJNA764181  SAMN21594074   \n",
       "SRR16040416        WGS         146  317852471  PRJNA764181  SAMN21594073   \n",
       "SRR16040417        WGS         146  534617403  PRJNA764181  SAMN21594072   \n",
       "SRR16040418        WGS         146  190807225  PRJNA764181  SAMN21594071   \n",
       "...                ...         ...        ...          ...           ...   \n",
       "SRR23686722        WGS         148  120274420  PRJNA764181  SAMN33567412   \n",
       "SRR23686724        WGS         152  136342632  PRJNA764181  SAMN33567393   \n",
       "SRR23686726        WGS         148  146166280  PRJNA764181  SAMN33567409   \n",
       "SRR23686727        WGS         152  207481824  PRJNA764181  SAMN33567408   \n",
       "SRR23686731        WGS         152  181081552  PRJNA764181  SAMN33567404   \n",
       "\n",
       "                                      BioSampleModel      Bytes  \\\n",
       "Run                                                               \n",
       "SRR16040414  SARS-CoV-2: clinical or host-associated   43635441   \n",
       "SRR16040415  SARS-CoV-2: clinical or host-associated   62921122   \n",
       "SRR16040416  SARS-CoV-2: clinical or host-associated  128538693   \n",
       "SRR16040417  SARS-CoV-2: clinical or host-associated  220484561   \n",
       "SRR16040418  SARS-CoV-2: clinical or host-associated   79077884   \n",
       "...                                              ...        ...   \n",
       "SRR23686722  SARS-CoV-2: clinical or host-associated   42683526   \n",
       "SRR23686724  SARS-CoV-2: clinical or host-associated   66649758   \n",
       "SRR23686726  SARS-CoV-2: clinical or host-associated   51732494   \n",
       "SRR23686727  SARS-CoV-2: clinical or host-associated  104162583   \n",
       "SRR23686731  SARS-CoV-2: clinical or host-associated   88330064   \n",
       "\n",
       "                                Center Name Collection_Date Consent  ...  \\\n",
       "Run                                                                  ...   \n",
       "SRR16040414  DISEASE PREVENTION AND CONTROL      2021-08-23  public  ...   \n",
       "SRR16040415  DISEASE PREVENTION AND CONTROL      2021-08-11  public  ...   \n",
       "SRR16040416  DISEASE PREVENTION AND CONTROL      2021-08-11  public  ...   \n",
       "SRR16040417  DISEASE PREVENTION AND CONTROL      2021-08-11  public  ...   \n",
       "SRR16040418  DISEASE PREVENTION AND CONTROL      2021-08-11  public  ...   \n",
       "...                                     ...             ...     ...  ...   \n",
       "SRR23686722  DISEASE PREVENTION AND CONTROL      2023-01-31  public  ...   \n",
       "SRR23686724  DISEASE PREVENTION AND CONTROL      2023-01-25  public  ...   \n",
       "SRR23686726  DISEASE PREVENTION AND CONTROL      2023-01-31  public  ...   \n",
       "SRR23686727  DISEASE PREVENTION AND CONTROL      2023-01-29  public  ...   \n",
       "SRR23686731  DISEASE PREVENTION AND CONTROL      2023-01-28  public  ...   \n",
       "\n",
       "                 raw_sequence_data_processing_method (run)  \\\n",
       "Run                                                          \n",
       "SRR16040414  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR16040415  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR16040416  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR16040417  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR16040418  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "...                                                    ...   \n",
       "SRR23686722  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR23686724  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR23686726  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR23686727  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR23686731  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "\n",
       "                      ReleaseDate           create_date version  \\\n",
       "Run                                                               \n",
       "SRR16040414  2021-09-24T00:00:00Z  2022-04-20T23:59:00Z       2   \n",
       "SRR16040415  2021-09-24T00:00:00Z  2022-04-21T00:00:00Z       2   \n",
       "SRR16040416  2021-09-24T00:00:00Z  2022-04-21T00:00:00Z       2   \n",
       "SRR16040417  2021-09-24T00:00:00Z  2022-04-21T00:01:00Z       2   \n",
       "SRR16040418  2021-09-24T00:00:00Z  2022-04-21T00:00:00Z       2   \n",
       "...                           ...                   ...     ...   \n",
       "SRR23686722  2023-03-02T00:00:00Z  2023-03-02T15:11:00Z       2   \n",
       "SRR23686724  2023-03-02T00:00:00Z  2023-03-02T15:11:00Z       2   \n",
       "SRR23686726  2023-03-02T00:00:00Z  2023-03-02T15:11:00Z       2   \n",
       "SRR23686727  2023-03-02T00:00:00Z  2023-03-02T15:11:00Z       2   \n",
       "SRR23686731  2023-03-02T00:00:00Z  2023-03-02T15:11:00Z       2   \n",
       "\n",
       "                    Sample Name  SRA Study  \\\n",
       "Run                                          \n",
       "SRR16040414  TX-HHD-210902C2794  SRP337649   \n",
       "SRR16040415   TX-HHD-2109027874  SRP337649   \n",
       "SRR16040416   TX-HHD-2109027848  SRP337649   \n",
       "SRR16040417   TX-HHD-2109027835  SRP337649   \n",
       "SRR16040418   TX-HHD-2109027827  SRP337649   \n",
       "...                         ...        ...   \n",
       "SRR23686722  TX-HHD-23020154868  SRP337649   \n",
       "SRR23686724   TX-HHD-2302021821  SRP337649   \n",
       "SRR23686726  TX-HHD-23020154860  SRP337649   \n",
       "SRR23686727   TX-HHD-2302024358  SRP337649   \n",
       "SRR23686731   TX-HHD-2302023836  SRP337649   \n",
       "\n",
       "                                               collected_by Host_age  \\\n",
       "Run                                                                    \n",
       "SRR16040414                         TSU - 3100 CLEBURNE ST.     18.0   \n",
       "SRR16040415             SOUTHWEST MSC- 6400 HIGH STAR DRIVE      1.0   \n",
       "SRR16040416             SOUTHWEST MSC- 6400 HIGH STAR DRIVE     12.0   \n",
       "SRR16040417             SOUTHWEST MSC- 6400 HIGH STAR DRIVE     48.0   \n",
       "SRR16040418             SOUTHWEST MSC- 6400 HIGH STAR DRIVE     30.0   \n",
       "...                                                     ...      ...   \n",
       "SRR23686722           MAGNOLIA HEALTH CENTER - 7037 CAPITOL     40.0   \n",
       "SRR23686724           MAGNOLIA HEALTH CENTER - 7037 CAPITOL     35.0   \n",
       "SRR23686726           MAGNOLIA HEALTH CENTER - 7037 CAPITOL     22.0   \n",
       "SRR23686727  HCO INST FORENSIC SCI - 1861 OLD SPANISH TRAIL     71.0   \n",
       "SRR23686731             SOUTHWEST MSC- 6400 HIGH STAR DRIVE     20.0   \n",
       "\n",
       "            amplicon__PCR_primer_scheme (run) host_sex  \n",
       "Run                                                     \n",
       "SRR16040414                               NaN     male  \n",
       "SRR16040415                               NaN     male  \n",
       "SRR16040416                               NaN   female  \n",
       "SRR16040417                               NaN   female  \n",
       "SRR16040418                               NaN   female  \n",
       "...                                       ...      ...  \n",
       "SRR23686722                           VarSkip     male  \n",
       "SRR23686724                           VarSkip   female  \n",
       "SRR23686726                           VarSkip   female  \n",
       "SRR23686727                           VarSkip     male  \n",
       "SRR23686731                           VarSkip   female  \n",
       "\n",
       "[10111 rows x 41 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "metadata = metadata[metadata['geo_loc_name'] == 'USA: Texas']\n",
    "metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "filtered_list = []\n",
    "for idx, row in metadata.iterrows():\n",
    "    if idx in sample_ids:\n",
    "        filtered_list.append(row)\n",
    "        \n",
    "filtered_metadata = pd.DataFrame(filtered_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "filtered_metadata = metadata.copy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    .dataframe tbody tr th:only-of-type {\n",
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       "    .dataframe thead th {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Assay Type</th>\n",
       "      <th>AvgSpotLen</th>\n",
       "      <th>Bases</th>\n",
       "      <th>BioProject</th>\n",
       "      <th>BioSample</th>\n",
       "      <th>BioSampleModel</th>\n",
       "      <th>Bytes</th>\n",
       "      <th>Center Name</th>\n",
       "      <th>Collection_Date</th>\n",
       "      <th>Consent</th>\n",
       "      <th>...</th>\n",
       "      <th>raw_sequence_data_processing_method (run)</th>\n",
       "      <th>ReleaseDate</th>\n",
       "      <th>create_date</th>\n",
       "      <th>version</th>\n",
       "      <th>Sample Name</th>\n",
       "      <th>SRA Study</th>\n",
       "      <th>collected_by</th>\n",
       "      <th>Host_age</th>\n",
       "      <th>amplicon__PCR_primer_scheme (run)</th>\n",
       "      <th>host_sex</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Run</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>SRR16040414</th>\n",
       "      <td>WGS</td>\n",
       "      <td>152</td>\n",
       "      <td>123142344</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN21593958</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>43635441</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-08-23</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-09-24T00:00:00Z</td>\n",
       "      <td>2022-04-20T23:59:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-210902C2794</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>TSU - 3100 CLEBURNE ST.</td>\n",
       "      <td>18.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>male</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR16040415</th>\n",
       "      <td>WGS</td>\n",
       "      <td>146</td>\n",
       "      <td>157571814</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN21594074</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>62921122</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-08-11</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-09-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:00:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2109027874</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>SOUTHWEST MSC- 6400 HIGH STAR DRIVE</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>male</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR16040416</th>\n",
       "      <td>WGS</td>\n",
       "      <td>146</td>\n",
       "      <td>317852471</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN21594073</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>128538693</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-08-11</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-09-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:00:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2109027848</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>SOUTHWEST MSC- 6400 HIGH STAR DRIVE</td>\n",
       "      <td>12.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR16040417</th>\n",
       "      <td>WGS</td>\n",
       "      <td>146</td>\n",
       "      <td>534617403</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN21594072</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>220484561</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-08-11</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-09-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:01:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2109027835</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>SOUTHWEST MSC- 6400 HIGH STAR DRIVE</td>\n",
       "      <td>48.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR16040418</th>\n",
       "      <td>WGS</td>\n",
       "      <td>146</td>\n",
       "      <td>190807225</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN21594071</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>79077884</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-08-11</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-09-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:00:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2109027827</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>SOUTHWEST MSC- 6400 HIGH STAR DRIVE</td>\n",
       "      <td>30.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR23686722</th>\n",
       "      <td>WGS</td>\n",
       "      <td>148</td>\n",
       "      <td>120274420</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN33567412</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>42683526</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2023-01-31</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2023-03-02T00:00:00Z</td>\n",
       "      <td>2023-03-02T15:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-23020154868</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>MAGNOLIA HEALTH CENTER - 7037 CAPITOL</td>\n",
       "      <td>40.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>male</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR23686724</th>\n",
       "      <td>WGS</td>\n",
       "      <td>152</td>\n",
       "      <td>136342632</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN33567393</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>66649758</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2023-01-25</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2023-03-02T00:00:00Z</td>\n",
       "      <td>2023-03-02T15:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2302021821</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>MAGNOLIA HEALTH CENTER - 7037 CAPITOL</td>\n",
       "      <td>35.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR23686726</th>\n",
       "      <td>WGS</td>\n",
       "      <td>148</td>\n",
       "      <td>146166280</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN33567409</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>51732494</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2023-01-31</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2023-03-02T00:00:00Z</td>\n",
       "      <td>2023-03-02T15:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-23020154860</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>MAGNOLIA HEALTH CENTER - 7037 CAPITOL</td>\n",
       "      <td>22.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR23686727</th>\n",
       "      <td>WGS</td>\n",
       "      <td>152</td>\n",
       "      <td>207481824</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN33567408</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>104162583</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2023-01-29</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2023-03-02T00:00:00Z</td>\n",
       "      <td>2023-03-02T15:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2302024358</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>HCO INST FORENSIC SCI - 1861 OLD SPANISH TRAIL</td>\n",
       "      <td>71.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>male</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR23686731</th>\n",
       "      <td>WGS</td>\n",
       "      <td>152</td>\n",
       "      <td>181081552</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN33567404</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>88330064</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2023-01-28</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2023-03-02T00:00:00Z</td>\n",
       "      <td>2023-03-02T15:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2302023836</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>SOUTHWEST MSC- 6400 HIGH STAR DRIVE</td>\n",
       "      <td>20.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>10111 rows × 41 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            Assay Type  AvgSpotLen      Bases   BioProject     BioSample  \\\n",
       "Run                                                                        \n",
       "SRR16040414        WGS         152  123142344  PRJNA764181  SAMN21593958   \n",
       "SRR16040415        WGS         146  157571814  PRJNA764181  SAMN21594074   \n",
       "SRR16040416        WGS         146  317852471  PRJNA764181  SAMN21594073   \n",
       "SRR16040417        WGS         146  534617403  PRJNA764181  SAMN21594072   \n",
       "SRR16040418        WGS         146  190807225  PRJNA764181  SAMN21594071   \n",
       "...                ...         ...        ...          ...           ...   \n",
       "SRR23686722        WGS         148  120274420  PRJNA764181  SAMN33567412   \n",
       "SRR23686724        WGS         152  136342632  PRJNA764181  SAMN33567393   \n",
       "SRR23686726        WGS         148  146166280  PRJNA764181  SAMN33567409   \n",
       "SRR23686727        WGS         152  207481824  PRJNA764181  SAMN33567408   \n",
       "SRR23686731        WGS         152  181081552  PRJNA764181  SAMN33567404   \n",
       "\n",
       "                                      BioSampleModel      Bytes  \\\n",
       "Run                                                               \n",
       "SRR16040414  SARS-CoV-2: clinical or host-associated   43635441   \n",
       "SRR16040415  SARS-CoV-2: clinical or host-associated   62921122   \n",
       "SRR16040416  SARS-CoV-2: clinical or host-associated  128538693   \n",
       "SRR16040417  SARS-CoV-2: clinical or host-associated  220484561   \n",
       "SRR16040418  SARS-CoV-2: clinical or host-associated   79077884   \n",
       "...                                              ...        ...   \n",
       "SRR23686722  SARS-CoV-2: clinical or host-associated   42683526   \n",
       "SRR23686724  SARS-CoV-2: clinical or host-associated   66649758   \n",
       "SRR23686726  SARS-CoV-2: clinical or host-associated   51732494   \n",
       "SRR23686727  SARS-CoV-2: clinical or host-associated  104162583   \n",
       "SRR23686731  SARS-CoV-2: clinical or host-associated   88330064   \n",
       "\n",
       "                                Center Name Collection_Date Consent  ...  \\\n",
       "Run                                                                  ...   \n",
       "SRR16040414  DISEASE PREVENTION AND CONTROL      2021-08-23  public  ...   \n",
       "SRR16040415  DISEASE PREVENTION AND CONTROL      2021-08-11  public  ...   \n",
       "SRR16040416  DISEASE PREVENTION AND CONTROL      2021-08-11  public  ...   \n",
       "SRR16040417  DISEASE PREVENTION AND CONTROL      2021-08-11  public  ...   \n",
       "SRR16040418  DISEASE PREVENTION AND CONTROL      2021-08-11  public  ...   \n",
       "...                                     ...             ...     ...  ...   \n",
       "SRR23686722  DISEASE PREVENTION AND CONTROL      2023-01-31  public  ...   \n",
       "SRR23686724  DISEASE PREVENTION AND CONTROL      2023-01-25  public  ...   \n",
       "SRR23686726  DISEASE PREVENTION AND CONTROL      2023-01-31  public  ...   \n",
       "SRR23686727  DISEASE PREVENTION AND CONTROL      2023-01-29  public  ...   \n",
       "SRR23686731  DISEASE PREVENTION AND CONTROL      2023-01-28  public  ...   \n",
       "\n",
       "                 raw_sequence_data_processing_method (run)  \\\n",
       "Run                                                          \n",
       "SRR16040414  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR16040415  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR16040416  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR16040417  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR16040418  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "...                                                    ...   \n",
       "SRR23686722  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR23686724  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR23686726  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR23686727  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR23686731  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "\n",
       "                      ReleaseDate           create_date version  \\\n",
       "Run                                                               \n",
       "SRR16040414  2021-09-24T00:00:00Z  2022-04-20T23:59:00Z       2   \n",
       "SRR16040415  2021-09-24T00:00:00Z  2022-04-21T00:00:00Z       2   \n",
       "SRR16040416  2021-09-24T00:00:00Z  2022-04-21T00:00:00Z       2   \n",
       "SRR16040417  2021-09-24T00:00:00Z  2022-04-21T00:01:00Z       2   \n",
       "SRR16040418  2021-09-24T00:00:00Z  2022-04-21T00:00:00Z       2   \n",
       "...                           ...                   ...     ...   \n",
       "SRR23686722  2023-03-02T00:00:00Z  2023-03-02T15:11:00Z       2   \n",
       "SRR23686724  2023-03-02T00:00:00Z  2023-03-02T15:11:00Z       2   \n",
       "SRR23686726  2023-03-02T00:00:00Z  2023-03-02T15:11:00Z       2   \n",
       "SRR23686727  2023-03-02T00:00:00Z  2023-03-02T15:11:00Z       2   \n",
       "SRR23686731  2023-03-02T00:00:00Z  2023-03-02T15:11:00Z       2   \n",
       "\n",
       "                    Sample Name  SRA Study  \\\n",
       "Run                                          \n",
       "SRR16040414  TX-HHD-210902C2794  SRP337649   \n",
       "SRR16040415   TX-HHD-2109027874  SRP337649   \n",
       "SRR16040416   TX-HHD-2109027848  SRP337649   \n",
       "SRR16040417   TX-HHD-2109027835  SRP337649   \n",
       "SRR16040418   TX-HHD-2109027827  SRP337649   \n",
       "...                         ...        ...   \n",
       "SRR23686722  TX-HHD-23020154868  SRP337649   \n",
       "SRR23686724   TX-HHD-2302021821  SRP337649   \n",
       "SRR23686726  TX-HHD-23020154860  SRP337649   \n",
       "SRR23686727   TX-HHD-2302024358  SRP337649   \n",
       "SRR23686731   TX-HHD-2302023836  SRP337649   \n",
       "\n",
       "                                               collected_by Host_age  \\\n",
       "Run                                                                    \n",
       "SRR16040414                         TSU - 3100 CLEBURNE ST.     18.0   \n",
       "SRR16040415             SOUTHWEST MSC- 6400 HIGH STAR DRIVE      1.0   \n",
       "SRR16040416             SOUTHWEST MSC- 6400 HIGH STAR DRIVE     12.0   \n",
       "SRR16040417             SOUTHWEST MSC- 6400 HIGH STAR DRIVE     48.0   \n",
       "SRR16040418             SOUTHWEST MSC- 6400 HIGH STAR DRIVE     30.0   \n",
       "...                                                     ...      ...   \n",
       "SRR23686722           MAGNOLIA HEALTH CENTER - 7037 CAPITOL     40.0   \n",
       "SRR23686724           MAGNOLIA HEALTH CENTER - 7037 CAPITOL     35.0   \n",
       "SRR23686726           MAGNOLIA HEALTH CENTER - 7037 CAPITOL     22.0   \n",
       "SRR23686727  HCO INST FORENSIC SCI - 1861 OLD SPANISH TRAIL     71.0   \n",
       "SRR23686731             SOUTHWEST MSC- 6400 HIGH STAR DRIVE     20.0   \n",
       "\n",
       "            amplicon__PCR_primer_scheme (run) host_sex  \n",
       "Run                                                     \n",
       "SRR16040414                               NaN     male  \n",
       "SRR16040415                               NaN     male  \n",
       "SRR16040416                               NaN   female  \n",
       "SRR16040417                               NaN   female  \n",
       "SRR16040418                               NaN   female  \n",
       "...                                       ...      ...  \n",
       "SRR23686722                           VarSkip     male  \n",
       "SRR23686724                           VarSkip   female  \n",
       "SRR23686726                           VarSkip   female  \n",
       "SRR23686727                           VarSkip     male  \n",
       "SRR23686731                           VarSkip   female  \n",
       "\n",
       "[10111 rows x 41 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "filtered_metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "filtered_metadata['Collection_Date'] =  pd.to_datetime(filtered_metadata['Collection_Date'], format='%Y-%m-%d')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Timestamp('2021-07-18 00:00:00')"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "filtered_metadata['Collection_Date'].min()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Timestamp('2023-02-21 00:00:00')"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "filtered_metadata['Collection_Date'].max()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [],
   "source": [
    "import datetime as dt\n",
    "\n",
    "start = filtered_metadata['Collection_Date'].min()\n",
    "end = start\n",
    "\n",
    "week_offset = dt.timedelta(days = 7)\n",
    "sample_counts = []\n",
    "x_ticklabels = []\n",
    "while end <= filtered_metadata['Collection_Date'].max():\n",
    "    #print(start, end)\n",
    "    end = start + week_offset\n",
    "    \n",
    "    weekly_clinical_df = filtered_metadata[(filtered_metadata['Collection_Date'] >= start) & (filtered_metadata['Collection_Date'] < end)]\n",
    "    weekly_sample_count = weekly_clinical_df.shape[0]\n",
    "    \n",
    "    x_ticklabels.append((start).strftime('%m-%d-%y'))\n",
    "    sample_counts.append(weekly_sample_count)\n",
    "    start = end\n",
    "    \n",
    "x_ticklabels.append((end).strftime('%m-%d-%y'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "84"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(sample_counts)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Text(0.5, 1.0, 'Clinical Sample Count')"
      ]
     },
     "execution_count": 40,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 1080x216 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "\n",
    "fontsize = 14\n",
    "fig, ax  = plt.subplots(1, 1, figsize=(15, 3), sharex=True, constrained_layout=True)\n",
    "\n",
    "x = np.arange(len(sample_counts))\n",
    "\n",
    "ax.bar(x, sample_counts, color='black', alpha=1, width=0.8)\n",
    "\n",
    "ax.set_ylim(0,2000)\n",
    "ax.set_xlim(-0.5,len(sample_counts)-0.5)\n",
    "ax.set_xticks(np.arange(len(sample_counts)+1)-0.5)\n",
    "ax.set_xticklabels(x_ticklabels, rotation=90, fontsize=12)\n",
    "\n",
    "ax.set_title('Clinical Sample Count')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "sampling_date_start = pd.to_datetime('12/06/2021')\n",
    "weekdays = timedelta(days=7)\n",
    "sampling_date_end = sampling_date_start + 8 * weekdays"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Timestamp('2022-01-31 00:00:00')"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sampling_date_end"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Assay Type</th>\n",
       "      <th>AvgSpotLen</th>\n",
       "      <th>Bases</th>\n",
       "      <th>BioProject</th>\n",
       "      <th>BioSample</th>\n",
       "      <th>BioSampleModel</th>\n",
       "      <th>Bytes</th>\n",
       "      <th>Center Name</th>\n",
       "      <th>Collection_Date</th>\n",
       "      <th>Consent</th>\n",
       "      <th>...</th>\n",
       "      <th>raw_sequence_data_processing_method (run)</th>\n",
       "      <th>ReleaseDate</th>\n",
       "      <th>create_date</th>\n",
       "      <th>version</th>\n",
       "      <th>Sample Name</th>\n",
       "      <th>SRA Study</th>\n",
       "      <th>collected_by</th>\n",
       "      <th>Host_age</th>\n",
       "      <th>amplicon__PCR_primer_scheme (run)</th>\n",
       "      <th>host_sex</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Run</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>SRR17385361</th>\n",
       "      <td>WGS</td>\n",
       "      <td>146</td>\n",
       "      <td>315053090</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN24526781</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>142251355</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-14</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-12-30T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2112218594</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>FBCCHS - COVID Testing - 4520 READING ROAD\\, S...</td>\n",
       "      <td>34.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR17385362</th>\n",
       "      <td>WGS</td>\n",
       "      <td>152</td>\n",
       "      <td>281371912</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN24526601</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>127877961</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-14</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-12-30T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2112208136</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>NaN</td>\n",
       "      <td>70.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR17385363</th>\n",
       "      <td>WGS</td>\n",
       "      <td>152</td>\n",
       "      <td>154251120</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN24526583</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>72785188</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-15</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-12-30T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2112200163</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>FBCCHS - COVID Testing - 4520 READING ROAD\\, S...</td>\n",
       "      <td>31.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR17385364</th>\n",
       "      <td>WGS</td>\n",
       "      <td>146</td>\n",
       "      <td>222184820</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN24526780</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>99844851</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-14</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-12-30T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2112218591</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>FBCCHS - COVID Testing - 4520 READING ROAD\\, S...</td>\n",
       "      <td>68.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR17385365</th>\n",
       "      <td>WGS</td>\n",
       "      <td>146</td>\n",
       "      <td>315530318</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN24526779</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>143143883</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-14</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-12-30T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2112218520</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>CAMBRIDGE HEALTH AND REHAB - 1106 GOLFVIEW DRIVE</td>\n",
       "      <td>53.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR18133353</th>\n",
       "      <td>WGS</td>\n",
       "      <td>148</td>\n",
       "      <td>362853376</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN26233067</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>152487576</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-22</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2022-02-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:23:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2201056720</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>GALE\\, LETOSHA</td>\n",
       "      <td>61.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR18133354</th>\n",
       "      <td>WGS</td>\n",
       "      <td>602</td>\n",
       "      <td>253916978</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN26232815</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>173718018</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-23</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2022-02-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:23:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2201141431</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>GALE\\, LETOSHA</td>\n",
       "      <td>9.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR18133355</th>\n",
       "      <td>WGS</td>\n",
       "      <td>148</td>\n",
       "      <td>195528424</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN26233066</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>80031811</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-22</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2022-02-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:22:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2201056655</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>GALE\\, LETOSHA</td>\n",
       "      <td>71.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR18133356</th>\n",
       "      <td>WGS</td>\n",
       "      <td>148</td>\n",
       "      <td>267667324</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN26233065</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>104782360</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-22</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2022-02-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:23:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2201146651</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>GALE\\, LETOSHA</td>\n",
       "      <td>25.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR18133357</th>\n",
       "      <td>WGS</td>\n",
       "      <td>148</td>\n",
       "      <td>203281996</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN26233064</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>83479895</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-22</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2022-02-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:23:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2201076632</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>GALE\\, LETOSHA</td>\n",
       "      <td>31.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5060 rows × 41 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            Assay Type  AvgSpotLen      Bases   BioProject     BioSample  \\\n",
       "Run                                                                        \n",
       "SRR17385361        WGS         146  315053090  PRJNA764181  SAMN24526781   \n",
       "SRR17385362        WGS         152  281371912  PRJNA764181  SAMN24526601   \n",
       "SRR17385363        WGS         152  154251120  PRJNA764181  SAMN24526583   \n",
       "SRR17385364        WGS         146  222184820  PRJNA764181  SAMN24526780   \n",
       "SRR17385365        WGS         146  315530318  PRJNA764181  SAMN24526779   \n",
       "...                ...         ...        ...          ...           ...   \n",
       "SRR18133353        WGS         148  362853376  PRJNA764181  SAMN26233067   \n",
       "SRR18133354        WGS         602  253916978  PRJNA764181  SAMN26232815   \n",
       "SRR18133355        WGS         148  195528424  PRJNA764181  SAMN26233066   \n",
       "SRR18133356        WGS         148  267667324  PRJNA764181  SAMN26233065   \n",
       "SRR18133357        WGS         148  203281996  PRJNA764181  SAMN26233064   \n",
       "\n",
       "                                      BioSampleModel      Bytes  \\\n",
       "Run                                                               \n",
       "SRR17385361  SARS-CoV-2: clinical or host-associated  142251355   \n",
       "SRR17385362  SARS-CoV-2: clinical or host-associated  127877961   \n",
       "SRR17385363  SARS-CoV-2: clinical or host-associated   72785188   \n",
       "SRR17385364  SARS-CoV-2: clinical or host-associated   99844851   \n",
       "SRR17385365  SARS-CoV-2: clinical or host-associated  143143883   \n",
       "...                                              ...        ...   \n",
       "SRR18133353  SARS-CoV-2: clinical or host-associated  152487576   \n",
       "SRR18133354  SARS-CoV-2: clinical or host-associated  173718018   \n",
       "SRR18133355  SARS-CoV-2: clinical or host-associated   80031811   \n",
       "SRR18133356  SARS-CoV-2: clinical or host-associated  104782360   \n",
       "SRR18133357  SARS-CoV-2: clinical or host-associated   83479895   \n",
       "\n",
       "                                Center Name Collection_Date Consent  ...  \\\n",
       "Run                                                                  ...   \n",
       "SRR17385361  DISEASE PREVENTION AND CONTROL      2021-12-14  public  ...   \n",
       "SRR17385362  DISEASE PREVENTION AND CONTROL      2021-12-14  public  ...   \n",
       "SRR17385363  DISEASE PREVENTION AND CONTROL      2021-12-15  public  ...   \n",
       "SRR17385364  DISEASE PREVENTION AND CONTROL      2021-12-14  public  ...   \n",
       "SRR17385365  DISEASE PREVENTION AND CONTROL      2021-12-14  public  ...   \n",
       "...                                     ...             ...     ...  ...   \n",
       "SRR18133353  DISEASE PREVENTION AND CONTROL      2021-12-22  public  ...   \n",
       "SRR18133354  DISEASE PREVENTION AND CONTROL      2021-12-23  public  ...   \n",
       "SRR18133355  DISEASE PREVENTION AND CONTROL      2021-12-22  public  ...   \n",
       "SRR18133356  DISEASE PREVENTION AND CONTROL      2021-12-22  public  ...   \n",
       "SRR18133357  DISEASE PREVENTION AND CONTROL      2021-12-22  public  ...   \n",
       "\n",
       "                 raw_sequence_data_processing_method (run)  \\\n",
       "Run                                                          \n",
       "SRR17385361  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR17385362  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR17385363  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR17385364  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR17385365  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "...                                                    ...   \n",
       "SRR18133353  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR18133354  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR18133355  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR18133356  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR18133357  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "\n",
       "                      ReleaseDate           create_date version  \\\n",
       "Run                                                               \n",
       "SRR17385361  2021-12-30T00:00:00Z  2022-04-21T00:11:00Z       2   \n",
       "SRR17385362  2021-12-30T00:00:00Z  2022-04-21T00:11:00Z       2   \n",
       "SRR17385363  2021-12-30T00:00:00Z  2022-04-21T00:11:00Z       2   \n",
       "SRR17385364  2021-12-30T00:00:00Z  2022-04-21T00:11:00Z       2   \n",
       "SRR17385365  2021-12-30T00:00:00Z  2022-04-21T00:11:00Z       2   \n",
       "...                           ...                   ...     ...   \n",
       "SRR18133353  2022-02-24T00:00:00Z  2022-04-21T00:23:00Z       2   \n",
       "SRR18133354  2022-02-24T00:00:00Z  2022-04-21T00:23:00Z       2   \n",
       "SRR18133355  2022-02-24T00:00:00Z  2022-04-21T00:22:00Z       2   \n",
       "SRR18133356  2022-02-24T00:00:00Z  2022-04-21T00:23:00Z       2   \n",
       "SRR18133357  2022-02-24T00:00:00Z  2022-04-21T00:23:00Z       2   \n",
       "\n",
       "                   Sample Name  SRA Study  \\\n",
       "Run                                         \n",
       "SRR17385361  TX-HHD-2112218594  SRP337649   \n",
       "SRR17385362  TX-HHD-2112208136  SRP337649   \n",
       "SRR17385363  TX-HHD-2112200163  SRP337649   \n",
       "SRR17385364  TX-HHD-2112218591  SRP337649   \n",
       "SRR17385365  TX-HHD-2112218520  SRP337649   \n",
       "...                        ...        ...   \n",
       "SRR18133353  TX-HHD-2201056720  SRP337649   \n",
       "SRR18133354  TX-HHD-2201141431  SRP337649   \n",
       "SRR18133355  TX-HHD-2201056655  SRP337649   \n",
       "SRR18133356  TX-HHD-2201146651  SRP337649   \n",
       "SRR18133357  TX-HHD-2201076632  SRP337649   \n",
       "\n",
       "                                                  collected_by Host_age  \\\n",
       "Run                                                                       \n",
       "SRR17385361  FBCCHS - COVID Testing - 4520 READING ROAD\\, S...     34.0   \n",
       "SRR17385362                                                NaN     70.0   \n",
       "SRR17385363  FBCCHS - COVID Testing - 4520 READING ROAD\\, S...     31.0   \n",
       "SRR17385364  FBCCHS - COVID Testing - 4520 READING ROAD\\, S...     68.0   \n",
       "SRR17385365   CAMBRIDGE HEALTH AND REHAB - 1106 GOLFVIEW DRIVE     53.0   \n",
       "...                                                        ...      ...   \n",
       "SRR18133353                                     GALE\\, LETOSHA     61.0   \n",
       "SRR18133354                                     GALE\\, LETOSHA      9.0   \n",
       "SRR18133355                                     GALE\\, LETOSHA     71.0   \n",
       "SRR18133356                                     GALE\\, LETOSHA     25.0   \n",
       "SRR18133357                                     GALE\\, LETOSHA     31.0   \n",
       "\n",
       "            amplicon__PCR_primer_scheme (run) host_sex  \n",
       "Run                                                     \n",
       "SRR17385361                               NaN   female  \n",
       "SRR17385362                               NaN      NaN  \n",
       "SRR17385363                               NaN   female  \n",
       "SRR17385364                               NaN   female  \n",
       "SRR17385365                               NaN   female  \n",
       "...                                       ...      ...  \n",
       "SRR18133353                           VarSkip      NaN  \n",
       "SRR18133354                           VarSkip      NaN  \n",
       "SRR18133355                           VarSkip      NaN  \n",
       "SRR18133356                           VarSkip      NaN  \n",
       "SRR18133357                           VarSkip      NaN  \n",
       "\n",
       "[5060 rows x 41 columns]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "filtered_metadata = filtered_metadata[(filtered_metadata['Collection_Date'] >= sampling_date_start) & (filtered_metadata['Collection_Date'] < sampling_date_end)]\n",
    "filtered_metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['Assay Type', 'AvgSpotLen', 'Bases', 'BioProject', 'BioSample',\n",
       "       'BioSampleModel', 'Bytes', 'Center Name', 'Collection_Date', 'Consent',\n",
       "       'DATASTORE filetype', 'DATASTORE provider', 'DATASTORE region',\n",
       "       'dehosting_method (run)', 'Experiment', 'geo_loc_name_country',\n",
       "       'geo_loc_name_country_continent', 'geo_loc_name', 'GISAID_virus_name',\n",
       "       'Host_disease', 'HOST', 'Instrument', 'Isolate', 'Isolation_source',\n",
       "       'Library Name', 'LibraryLayout', 'LibrarySelection', 'LibrarySource',\n",
       "       'Organism', 'Platform', 'purpose_of_sequencing',\n",
       "       'raw_sequence_data_processing_method (run)', 'ReleaseDate',\n",
       "       'create_date', 'version', 'Sample Name', 'SRA Study', 'collected_by',\n",
       "       'Host_age', 'amplicon__PCR_primer_scheme (run)', 'host_sex'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "filtered_metadata.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['FBCCHS - COVID Testing - 4520 READING ROAD\\\\, SUITE A-200', nan,\n",
       "       'CAMBRIDGE HEALTH AND REHAB - 1106 GOLFVIEW DRIVE',\n",
       "       'HARRIS CO. JUV. DET. CTR. - 1200 CONGRESS',\n",
       "       'PARK MANOR WESTCHASE - 11910 RICHMOND AVE',\n",
       "       'BRAZOS TOWERS BAYOU MANOR - 4141 S BRAESWOOD',\n",
       "       'HCO INST FORENSIC SCI - 1861 OLD SPANISH TRAIL',\n",
       "       \"MAYOR'S OFFICE - 8000 NORTH STADIUM DRIVE\",\n",
       "       'ACRES HOME MSC - 6719 W MONTGOMERY RD',\n",
       "       'HIRAM CLARKE MSC - 3810 W FUQUA ST',\n",
       "       'MEMORIAL HERMANN - 6411 FANNIN', 'TSU - 3100 CLEBURNE ST.',\n",
       "       'SOUTHWEST MSC- 6400 HIGH STAR DRIVE',\n",
       "       'SEVEN ACRES JEWISH - 6200 N BRAESWOOD BLVD',\n",
       "       'WINDSOR HOUSTON- 6920 T C Jester Blvd',\n",
       "       'NORTH HOUSTON - 9814 GRANT RD',\n",
       "       'MAGNOLIA HEALTH CENTER - 7037 CAPITOL',\n",
       "       'FORT BEND JUVENILE - 122 GOLFVIEW', 'GALE\\\\, LETOSHA',\n",
       "       'BROOKDALE WILLOWBROOKE - 13500 BRETON RIDGE ST',\n",
       "       'MEMORIAL CITY HEALTH- 1341 BLALOCK RD',\n",
       "       'THE HALLMARK - 4718 HALLMARK DR',\n",
       "       'BROOKDALE GALLERIA - 2929 POST OAK BOULEVARD',\n",
       "       'ROSENBERG H & R CENTER - 1419 MAHLMAN STREET',\n",
       "       'FORT BEND MEDICAL\\\\, EXAMINERS - 3840 BAMORE RD.',\n",
       "       'HOUSTON TRANSITIONAL-8550 JASON ST',\n",
       "       'PARK MANOR OF SOUTH - 11902 RESOURCE PKWY',\n",
       "       'FORT BEND COUNTY JAIL - 1410 RICHMOND PARKWAY',\n",
       "       'THE CONCIERGE- 2310 Eldridge Pkwy S',\n",
       "       'KIRBY - 9250 KIRBY DRIVE\\\\, 2030',\n",
       "       'HOUSTON TRANSITIONAL-8550 Jason St',\n",
       "       'THE MEDICAL RESORT - 13220 BRETON RIDGE STREET',\n",
       "       'RONALD McDONALD HOUSE - 8000 N. STADIUM DRIVE',\n",
       "       'FORT BEND EMPLOYEE - 301 JACKSON STREET',\n",
       "       'GALVESTON COUNTY HLTH DST - PO BOX 939',\n",
       "       'PARADISE LIVING - 7639 BEECHNUT LIVING',\n",
       "       'INCARNATE WORD CONVENT - 3400 BRADFORD STREET',\n",
       "       'DEERBROOK SKILLED NURSING - 9250 HUMBLE-WESTFIELD ROAD',\n",
       "       'FARRINGTON AT TANGLEWOOD - 505 BERING DRIVE',\n",
       "       'HARRIS CO JUV DET CTR- 1200 Congress St',\n",
       "       'FORT BEND CO. HEALTH DEPT - 4520 READING ROAD',\n",
       "       'required_for_submission'], dtype=object)"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "filtered_metadata['collected_by'].unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2021-12-06 00:00:00 2021-12-13 00:00:00 64\n",
      "2021-12-13 00:00:00 2021-12-20 00:00:00 365\n",
      "2021-12-20 00:00:00 2021-12-27 00:00:00 853\n",
      "2021-12-27 00:00:00 2022-01-03 00:00:00 1657\n",
      "2022-01-03 00:00:00 2022-01-10 00:00:00 1081\n",
      "2022-01-10 00:00:00 2022-01-17 00:00:00 628\n",
      "2022-01-17 00:00:00 2022-01-24 00:00:00 248\n",
      "2022-01-24 00:00:00 2022-01-31 00:00:00 164\n"
     ]
    }
   ],
   "source": [
    "for i in range(0, 8):\n",
    "    start = sampling_date_start + i*weekdays\n",
    "    end = sampling_date_start + (i+1)*weekdays\n",
    "    \n",
    "    weekly_sample_count = filtered_metadata[(filtered_metadata['Collection_Date'] >= start) & (filtered_metadata['Collection_Date'] < end)].shape[0]\n",
    "    print(start, end, weekly_sample_count)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "# for i, sra_id in enumerate(filtered_metadata.index.to_list()):\n",
    "#     with open(os.path.join(f\"/home/Users/yl181/cdc_harvest_variants/Proposed_Pipeline_SRA_Inputs_Quarc\", f\"hv_job_{i}.in\"), \"w\") as array_out:\n",
    "#         array_out.write(sra_id)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "with open(\"houston_sampled_sra.txt\", 'w') as output_f:\n",
    "    for sra_id in filtered_metadata.index.to_list():\n",
    "        output_f.write(f\"{sra_id}\\n\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "#filtered_metadata.to_csv('PRJNA764181.filtered.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    .dataframe tbody tr th:only-of-type {\n",
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       "    .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>Assay Type</th>\n",
       "      <th>AvgSpotLen</th>\n",
       "      <th>Bases</th>\n",
       "      <th>BioProject</th>\n",
       "      <th>BioSample</th>\n",
       "      <th>BioSampleModel</th>\n",
       "      <th>Bytes</th>\n",
       "      <th>Center Name</th>\n",
       "      <th>Collection_Date</th>\n",
       "      <th>Consent</th>\n",
       "      <th>...</th>\n",
       "      <th>raw_sequence_data_processing_method (run)</th>\n",
       "      <th>ReleaseDate</th>\n",
       "      <th>create_date</th>\n",
       "      <th>version</th>\n",
       "      <th>Sample Name</th>\n",
       "      <th>SRA Study</th>\n",
       "      <th>collected_by</th>\n",
       "      <th>Host_age</th>\n",
       "      <th>amplicon__PCR_primer_scheme (run)</th>\n",
       "      <th>host_sex</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Run</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>SRR17385361</th>\n",
       "      <td>WGS</td>\n",
       "      <td>146</td>\n",
       "      <td>315053090</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN24526781</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>142251355</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-14</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-12-30T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2112218594</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>FBCCHS - COVID Testing - 4520 READING ROAD\\, S...</td>\n",
       "      <td>34.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR17385362</th>\n",
       "      <td>WGS</td>\n",
       "      <td>152</td>\n",
       "      <td>281371912</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN24526601</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>127877961</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-14</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-12-30T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2112208136</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>NaN</td>\n",
       "      <td>70.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR17385363</th>\n",
       "      <td>WGS</td>\n",
       "      <td>152</td>\n",
       "      <td>154251120</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN24526583</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>72785188</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-15</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-12-30T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2112200163</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>FBCCHS - COVID Testing - 4520 READING ROAD\\, S...</td>\n",
       "      <td>31.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR17385364</th>\n",
       "      <td>WGS</td>\n",
       "      <td>146</td>\n",
       "      <td>222184820</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN24526780</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>99844851</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-14</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-12-30T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2112218591</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>FBCCHS - COVID Testing - 4520 READING ROAD\\, S...</td>\n",
       "      <td>68.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR17385365</th>\n",
       "      <td>WGS</td>\n",
       "      <td>146</td>\n",
       "      <td>315530318</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN24526779</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>143143883</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-14</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2021-12-30T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:11:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2112218520</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>CAMBRIDGE HEALTH AND REHAB - 1106 GOLFVIEW DRIVE</td>\n",
       "      <td>53.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>female</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR18133353</th>\n",
       "      <td>WGS</td>\n",
       "      <td>148</td>\n",
       "      <td>362853376</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN26233067</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>152487576</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-22</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2022-02-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:23:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2201056720</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>GALE\\, LETOSHA</td>\n",
       "      <td>61.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR18133354</th>\n",
       "      <td>WGS</td>\n",
       "      <td>602</td>\n",
       "      <td>253916978</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN26232815</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>173718018</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-23</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2022-02-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:23:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2201141431</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>GALE\\, LETOSHA</td>\n",
       "      <td>9.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR18133355</th>\n",
       "      <td>WGS</td>\n",
       "      <td>148</td>\n",
       "      <td>195528424</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN26233066</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>80031811</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-22</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2022-02-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:22:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2201056655</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>GALE\\, LETOSHA</td>\n",
       "      <td>71.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR18133356</th>\n",
       "      <td>WGS</td>\n",
       "      <td>148</td>\n",
       "      <td>267667324</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN26233065</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>104782360</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-22</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2022-02-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:23:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2201146651</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>GALE\\, LETOSHA</td>\n",
       "      <td>25.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SRR18133357</th>\n",
       "      <td>WGS</td>\n",
       "      <td>148</td>\n",
       "      <td>203281996</td>\n",
       "      <td>PRJNA764181</td>\n",
       "      <td>SAMN26233064</td>\n",
       "      <td>SARS-CoV-2: clinical or host-associated</td>\n",
       "      <td>83479895</td>\n",
       "      <td>DISEASE PREVENTION AND CONTROL</td>\n",
       "      <td>2021-12-22</td>\n",
       "      <td>public</td>\n",
       "      <td>...</td>\n",
       "      <td>BWA Version: 0.7.17-r1188; iVar version 1.2.2</td>\n",
       "      <td>2022-02-24T00:00:00Z</td>\n",
       "      <td>2022-04-21T00:23:00Z</td>\n",
       "      <td>2</td>\n",
       "      <td>TX-HHD-2201076632</td>\n",
       "      <td>SRP337649</td>\n",
       "      <td>GALE\\, LETOSHA</td>\n",
       "      <td>31.0</td>\n",
       "      <td>VarSkip</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5060 rows × 41 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            Assay Type  AvgSpotLen      Bases   BioProject     BioSample  \\\n",
       "Run                                                                        \n",
       "SRR17385361        WGS         146  315053090  PRJNA764181  SAMN24526781   \n",
       "SRR17385362        WGS         152  281371912  PRJNA764181  SAMN24526601   \n",
       "SRR17385363        WGS         152  154251120  PRJNA764181  SAMN24526583   \n",
       "SRR17385364        WGS         146  222184820  PRJNA764181  SAMN24526780   \n",
       "SRR17385365        WGS         146  315530318  PRJNA764181  SAMN24526779   \n",
       "...                ...         ...        ...          ...           ...   \n",
       "SRR18133353        WGS         148  362853376  PRJNA764181  SAMN26233067   \n",
       "SRR18133354        WGS         602  253916978  PRJNA764181  SAMN26232815   \n",
       "SRR18133355        WGS         148  195528424  PRJNA764181  SAMN26233066   \n",
       "SRR18133356        WGS         148  267667324  PRJNA764181  SAMN26233065   \n",
       "SRR18133357        WGS         148  203281996  PRJNA764181  SAMN26233064   \n",
       "\n",
       "                                      BioSampleModel      Bytes  \\\n",
       "Run                                                               \n",
       "SRR17385361  SARS-CoV-2: clinical or host-associated  142251355   \n",
       "SRR17385362  SARS-CoV-2: clinical or host-associated  127877961   \n",
       "SRR17385363  SARS-CoV-2: clinical or host-associated   72785188   \n",
       "SRR17385364  SARS-CoV-2: clinical or host-associated   99844851   \n",
       "SRR17385365  SARS-CoV-2: clinical or host-associated  143143883   \n",
       "...                                              ...        ...   \n",
       "SRR18133353  SARS-CoV-2: clinical or host-associated  152487576   \n",
       "SRR18133354  SARS-CoV-2: clinical or host-associated  173718018   \n",
       "SRR18133355  SARS-CoV-2: clinical or host-associated   80031811   \n",
       "SRR18133356  SARS-CoV-2: clinical or host-associated  104782360   \n",
       "SRR18133357  SARS-CoV-2: clinical or host-associated   83479895   \n",
       "\n",
       "                                Center Name Collection_Date Consent  ...  \\\n",
       "Run                                                                  ...   \n",
       "SRR17385361  DISEASE PREVENTION AND CONTROL      2021-12-14  public  ...   \n",
       "SRR17385362  DISEASE PREVENTION AND CONTROL      2021-12-14  public  ...   \n",
       "SRR17385363  DISEASE PREVENTION AND CONTROL      2021-12-15  public  ...   \n",
       "SRR17385364  DISEASE PREVENTION AND CONTROL      2021-12-14  public  ...   \n",
       "SRR17385365  DISEASE PREVENTION AND CONTROL      2021-12-14  public  ...   \n",
       "...                                     ...             ...     ...  ...   \n",
       "SRR18133353  DISEASE PREVENTION AND CONTROL      2021-12-22  public  ...   \n",
       "SRR18133354  DISEASE PREVENTION AND CONTROL      2021-12-23  public  ...   \n",
       "SRR18133355  DISEASE PREVENTION AND CONTROL      2021-12-22  public  ...   \n",
       "SRR18133356  DISEASE PREVENTION AND CONTROL      2021-12-22  public  ...   \n",
       "SRR18133357  DISEASE PREVENTION AND CONTROL      2021-12-22  public  ...   \n",
       "\n",
       "                 raw_sequence_data_processing_method (run)  \\\n",
       "Run                                                          \n",
       "SRR17385361  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR17385362  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR17385363  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR17385364  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR17385365  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "...                                                    ...   \n",
       "SRR18133353  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR18133354  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR18133355  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR18133356  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "SRR18133357  BWA Version: 0.7.17-r1188; iVar version 1.2.2   \n",
       "\n",
       "                      ReleaseDate           create_date version  \\\n",
       "Run                                                               \n",
       "SRR17385361  2021-12-30T00:00:00Z  2022-04-21T00:11:00Z       2   \n",
       "SRR17385362  2021-12-30T00:00:00Z  2022-04-21T00:11:00Z       2   \n",
       "SRR17385363  2021-12-30T00:00:00Z  2022-04-21T00:11:00Z       2   \n",
       "SRR17385364  2021-12-30T00:00:00Z  2022-04-21T00:11:00Z       2   \n",
       "SRR17385365  2021-12-30T00:00:00Z  2022-04-21T00:11:00Z       2   \n",
       "...                           ...                   ...     ...   \n",
       "SRR18133353  2022-02-24T00:00:00Z  2022-04-21T00:23:00Z       2   \n",
       "SRR18133354  2022-02-24T00:00:00Z  2022-04-21T00:23:00Z       2   \n",
       "SRR18133355  2022-02-24T00:00:00Z  2022-04-21T00:22:00Z       2   \n",
       "SRR18133356  2022-02-24T00:00:00Z  2022-04-21T00:23:00Z       2   \n",
       "SRR18133357  2022-02-24T00:00:00Z  2022-04-21T00:23:00Z       2   \n",
       "\n",
       "                   Sample Name  SRA Study  \\\n",
       "Run                                         \n",
       "SRR17385361  TX-HHD-2112218594  SRP337649   \n",
       "SRR17385362  TX-HHD-2112208136  SRP337649   \n",
       "SRR17385363  TX-HHD-2112200163  SRP337649   \n",
       "SRR17385364  TX-HHD-2112218591  SRP337649   \n",
       "SRR17385365  TX-HHD-2112218520  SRP337649   \n",
       "...                        ...        ...   \n",
       "SRR18133353  TX-HHD-2201056720  SRP337649   \n",
       "SRR18133354  TX-HHD-2201141431  SRP337649   \n",
       "SRR18133355  TX-HHD-2201056655  SRP337649   \n",
       "SRR18133356  TX-HHD-2201146651  SRP337649   \n",
       "SRR18133357  TX-HHD-2201076632  SRP337649   \n",
       "\n",
       "                                                  collected_by Host_age  \\\n",
       "Run                                                                       \n",
       "SRR17385361  FBCCHS - COVID Testing - 4520 READING ROAD\\, S...     34.0   \n",
       "SRR17385362                                                NaN     70.0   \n",
       "SRR17385363  FBCCHS - COVID Testing - 4520 READING ROAD\\, S...     31.0   \n",
       "SRR17385364  FBCCHS - COVID Testing - 4520 READING ROAD\\, S...     68.0   \n",
       "SRR17385365   CAMBRIDGE HEALTH AND REHAB - 1106 GOLFVIEW DRIVE     53.0   \n",
       "...                                                        ...      ...   \n",
       "SRR18133353                                     GALE\\, LETOSHA     61.0   \n",
       "SRR18133354                                     GALE\\, LETOSHA      9.0   \n",
       "SRR18133355                                     GALE\\, LETOSHA     71.0   \n",
       "SRR18133356                                     GALE\\, LETOSHA     25.0   \n",
       "SRR18133357                                     GALE\\, LETOSHA     31.0   \n",
       "\n",
       "            amplicon__PCR_primer_scheme (run) host_sex  \n",
       "Run                                                     \n",
       "SRR17385361                               NaN   female  \n",
       "SRR17385362                               NaN      NaN  \n",
       "SRR17385363                               NaN   female  \n",
       "SRR17385364                               NaN   female  \n",
       "SRR17385365                               NaN   female  \n",
       "...                                       ...      ...  \n",
       "SRR18133353                           VarSkip      NaN  \n",
       "SRR18133354                           VarSkip      NaN  \n",
       "SRR18133355                           VarSkip      NaN  \n",
       "SRR18133356                           VarSkip      NaN  \n",
       "SRR18133357                           VarSkip      NaN  \n",
       "\n",
       "[5060 rows x 41 columns]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "filtered_metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "output_dir = '/home/Users/yl181/cdc_harvest_variants/Proposed_Pipeline_SRA_Outputs_Quarc'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "metadata": {},
   "outputs": [],
   "source": [
    "count = 0\n",
    "for i in range(5060):\n",
    "    if os.path.exists(f\"{output_dir}/{i}_out/cryptic_bam_files\"):\n",
    "        count += 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5050"
      ]
     },
     "execution_count": 69,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "count"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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