BioSample_and_SRA.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Make BioSample table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "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>T</th>\n",
       "      <th>Date</th>\n",
       "      <th>Bath</th>\n",
       "      <th>Tank</th>\n",
       "      <th>SourceSite</th>\n",
       "      <th>Extract</th>\n",
       "      <th>Temp</th>\n",
       "      <th>Nutrients</th>\n",
       "      <th>Fraction</th>\n",
       "      <th>BathName</th>\n",
       "      <th>TP</th>\n",
       "      <th>TP_Bath</th>\n",
       "      <th>TP_Bath_Site</th>\n",
       "      <th>Bath_Site</th>\n",
       "      <th>Partition</th>\n",
       "      <th>Treatment</th>\n",
       "      <th>SiteNumeric</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>#SampleID</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",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [T, Date, Bath, Tank, SourceSite, Extract, Temp, Nutrients, Fraction, BathName, TP, TP_Bath, TP_Bath_Site, Bath_Site, Partition, Treatment, SiteNumeric]\n",
       "Index: []"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [],
   "source": [
    "from qiime2 import Artifact\n",
    "\n",
    "table = Artifact.load('DIVERSITY_epiphytes/rarefied_table.qza').view(pd.DataFrame)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "mkdir: cannot create directory ‘biosample_sra’: File exists\n",
      "AS2214\n",
      "AS2202\n",
      "AS2084\n",
      "Tank-3B\n",
      "AS2004\n",
      "Tank-7C\n",
      "Tank-8C\n",
      "AS2055\n",
      "Tank-8B\n",
      "Tank-2B\n",
      "Tank-8A\n",
      "Tank-17A\n",
      "Tank-17B\n",
      "Tank-7D\n",
      "AS2201\n",
      "Tank-3D\n",
      "AS2200\n",
      "Tank-2A\n",
      "NTC-22\n",
      "Tank-7A\n",
      "AS2213\n",
      "AS2217\n",
      "Tank-16D\n",
      "Tank-17C\n",
      "AS2203\n",
      "Tank-13D\n",
      "Tank-12B\n",
      "Tank-13B\n",
      "Tank-16B\n",
      "Tank-2D\n",
      "Tank-12C\n",
      "NTC-PCR21\n",
      "Tank-16C\n",
      "NTC-PCR22\n",
      "AS2215\n",
      "Tank-7B\n",
      "NTC-21\n",
      "Tank-13C\n",
      "Tank-12A\n",
      "Tank-16A\n",
      "AS2212\n",
      "Tank-12D\n",
      "Tank-2C\n",
      "Tank-17D\n",
      "Tank-3C\n",
      "Tank-13A\n",
      "Tank-3A\n",
      "Tank-8D\n",
      "AS2205\n"
     ]
    },
    {
     "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>replicate</th>\n",
       "      <th>description</th>\n",
       "      <th>*geo_loc_name</th>\n",
       "      <th>*host</th>\n",
       "      <th>*collection_date</th>\n",
       "      <th>sample_title</th>\n",
       "      <th>*organism</th>\n",
       "      <th>*env_medium</th>\n",
       "      <th>*lat_lon</th>\n",
       "      <th>*env_broad_scale</th>\n",
       "      <th>*env_local_scale</th>\n",
       "      <th>source_site</th>\n",
       "      <th>treatment</th>\n",
       "      <th>time point</th>\n",
       "      <th>original_id</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>*sample_name</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>AS2003</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>Halophila stipulacea</td>\n",
       "      <td>15-Aug-2019</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>epiphytic metagenome</td>\n",
       "      <td>water</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>SB</td>\n",
       "      <td>CTCN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>AS2003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AS2067</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>Halophila stipulacea</td>\n",
       "      <td>08-Sep-2019</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>epiphytic metagenome</td>\n",
       "      <td>water</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>SB</td>\n",
       "      <td>TCN</td>\n",
       "      <td>3.0</td>\n",
       "      <td>AS2067</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AS2103</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>Halophila stipulacea</td>\n",
       "      <td>22-Sep-2019</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>epiphytic metagenome</td>\n",
       "      <td>water</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>SB</td>\n",
       "      <td>TCN</td>\n",
       "      <td>5.0</td>\n",
       "      <td>AS2103</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AS2011</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>Halophila stipulacea</td>\n",
       "      <td>15-Aug-2019</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>epiphytic metagenome</td>\n",
       "      <td>water</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>SB</td>\n",
       "      <td>CTN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>AS2011</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AS2076</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>Halophila stipulacea</td>\n",
       "      <td>08-Sep-2019</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>epiphytic metagenome</td>\n",
       "      <td>water</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>TY</td>\n",
       "      <td>TN</td>\n",
       "      <td>3.0</td>\n",
       "      <td>AS2076</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AS2058</th>\n",
       "      <td>biological replicate 4</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>Halophila stipulacea</td>\n",
       "      <td>08-Sep-2019</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>epiphytic metagenome</td>\n",
       "      <td>water</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>SB</td>\n",
       "      <td>CTN</td>\n",
       "      <td>3.0</td>\n",
       "      <td>AS2058</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AS2159</th>\n",
       "      <td>biological replicate 4</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>Halophila stipulacea</td>\n",
       "      <td>13-Oct-2019</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>epiphytic metagenome</td>\n",
       "      <td>water</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>SB</td>\n",
       "      <td>TN</td>\n",
       "      <td>8.0</td>\n",
       "      <td>AS2159</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AS2017</th>\n",
       "      <td>biological replicate 5</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>Halophila stipulacea</td>\n",
       "      <td>15-Aug-2019</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>epiphytic metagenome</td>\n",
       "      <td>water</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>TY</td>\n",
       "      <td>CTN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>AS2017</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AS2052</th>\n",
       "      <td>biological replicate 5</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>Halophila stipulacea</td>\n",
       "      <td>08-Sep-2019</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>epiphytic metagenome</td>\n",
       "      <td>water</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>TY</td>\n",
       "      <td>CTN</td>\n",
       "      <td>3.0</td>\n",
       "      <td>AS2052</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AS2075</th>\n",
       "      <td>biological replicate 4</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>Halophila stipulacea</td>\n",
       "      <td>08-Sep-2019</td>\n",
       "      <td>Epiphytic metagenome sample from Halophila sti...</td>\n",
       "      <td>epiphytic metagenome</td>\n",
       "      <td>water</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>SB</td>\n",
       "      <td>TN</td>\n",
       "      <td>3.0</td>\n",
       "      <td>AS2075</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>140 rows × 15 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                           replicate  \\\n",
       "*sample_name                           \n",
       "AS2003        biological replicate 1   \n",
       "AS2067        biological replicate 1   \n",
       "AS2103        biological replicate 1   \n",
       "AS2011        biological replicate 1   \n",
       "AS2076        biological replicate 1   \n",
       "...                              ...   \n",
       "AS2058        biological replicate 4   \n",
       "AS2159        biological replicate 4   \n",
       "AS2017        biological replicate 5   \n",
       "AS2052        biological replicate 5   \n",
       "AS2075        biological replicate 4   \n",
       "\n",
       "                                                    description  \\\n",
       "*sample_name                                                      \n",
       "AS2003        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2067        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2103        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2011        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2076        Epiphytic metagenome sample from Halophila sti...   \n",
       "...                                                         ...   \n",
       "AS2058        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2159        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2017        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2052        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2075        Epiphytic metagenome sample from Halophila sti...   \n",
       "\n",
       "                                            *geo_loc_name  \\\n",
       "*sample_name                                                \n",
       "AS2003        Israel:Hatzeva,DeadSeaAndAravaScienceCenter   \n",
       "AS2067        Israel:Hatzeva,DeadSeaAndAravaScienceCenter   \n",
       "AS2103        Israel:Hatzeva,DeadSeaAndAravaScienceCenter   \n",
       "AS2011        Israel:Hatzeva,DeadSeaAndAravaScienceCenter   \n",
       "AS2076        Israel:Hatzeva,DeadSeaAndAravaScienceCenter   \n",
       "...                                                   ...   \n",
       "AS2058        Israel:Hatzeva,DeadSeaAndAravaScienceCenter   \n",
       "AS2159        Israel:Hatzeva,DeadSeaAndAravaScienceCenter   \n",
       "AS2017        Israel:Hatzeva,DeadSeaAndAravaScienceCenter   \n",
       "AS2052        Israel:Hatzeva,DeadSeaAndAravaScienceCenter   \n",
       "AS2075        Israel:Hatzeva,DeadSeaAndAravaScienceCenter   \n",
       "\n",
       "                             *host *collection_date  \\\n",
       "*sample_name                                          \n",
       "AS2003        Halophila stipulacea      15-Aug-2019   \n",
       "AS2067        Halophila stipulacea      08-Sep-2019   \n",
       "AS2103        Halophila stipulacea      22-Sep-2019   \n",
       "AS2011        Halophila stipulacea      15-Aug-2019   \n",
       "AS2076        Halophila stipulacea      08-Sep-2019   \n",
       "...                            ...              ...   \n",
       "AS2058        Halophila stipulacea      08-Sep-2019   \n",
       "AS2159        Halophila stipulacea      13-Oct-2019   \n",
       "AS2017        Halophila stipulacea      15-Aug-2019   \n",
       "AS2052        Halophila stipulacea      08-Sep-2019   \n",
       "AS2075        Halophila stipulacea      08-Sep-2019   \n",
       "\n",
       "                                                   sample_title  \\\n",
       "*sample_name                                                      \n",
       "AS2003        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2067        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2103        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2011        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2076        Epiphytic metagenome sample from Halophila sti...   \n",
       "...                                                         ...   \n",
       "AS2058        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2159        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2017        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2052        Epiphytic metagenome sample from Halophila sti...   \n",
       "AS2075        Epiphytic metagenome sample from Halophila sti...   \n",
       "\n",
       "                         *organism *env_medium         *lat_lon  \\\n",
       "*sample_name                                                      \n",
       "AS2003        epiphytic metagenome       water  30.77 N 35.24 E   \n",
       "AS2067        epiphytic metagenome       water  30.77 N 35.24 E   \n",
       "AS2103        epiphytic metagenome       water  30.77 N 35.24 E   \n",
       "AS2011        epiphytic metagenome       water  30.77 N 35.24 E   \n",
       "AS2076        epiphytic metagenome       water  30.77 N 35.24 E   \n",
       "...                            ...         ...              ...   \n",
       "AS2058        epiphytic metagenome       water  30.77 N 35.24 E   \n",
       "AS2159        epiphytic metagenome       water  30.77 N 35.24 E   \n",
       "AS2017        epiphytic metagenome       water  30.77 N 35.24 E   \n",
       "AS2052        epiphytic metagenome       water  30.77 N 35.24 E   \n",
       "AS2075        epiphytic metagenome       water  30.77 N 35.24 E   \n",
       "\n",
       "                    *env_broad_scale     *env_local_scale source_site  \\\n",
       "*sample_name                                                            \n",
       "AS2003        marine seagrass meadow  mesocosm experiment          SB   \n",
       "AS2067        marine seagrass meadow  mesocosm experiment          SB   \n",
       "AS2103        marine seagrass meadow  mesocosm experiment          SB   \n",
       "AS2011        marine seagrass meadow  mesocosm experiment          SB   \n",
       "AS2076        marine seagrass meadow  mesocosm experiment          TY   \n",
       "...                              ...                  ...         ...   \n",
       "AS2058        marine seagrass meadow  mesocosm experiment          SB   \n",
       "AS2159        marine seagrass meadow  mesocosm experiment          SB   \n",
       "AS2017        marine seagrass meadow  mesocosm experiment          TY   \n",
       "AS2052        marine seagrass meadow  mesocosm experiment          TY   \n",
       "AS2075        marine seagrass meadow  mesocosm experiment          SB   \n",
       "\n",
       "             treatment  time point original_id  \n",
       "*sample_name                                    \n",
       "AS2003            CTCN         0.0      AS2003  \n",
       "AS2067             TCN         3.0      AS2067  \n",
       "AS2103             TCN         5.0      AS2103  \n",
       "AS2011             CTN         0.0      AS2011  \n",
       "AS2076              TN         3.0      AS2076  \n",
       "...                ...         ...         ...  \n",
       "AS2058             CTN         3.0      AS2058  \n",
       "AS2159              TN         8.0      AS2159  \n",
       "AS2017             CTN         0.0      AS2017  \n",
       "AS2052             CTN         3.0      AS2052  \n",
       "AS2075              TN         3.0      AS2075  \n",
       "\n",
       "[140 rows x 15 columns]"
      ]
     },
     "execution_count": 42,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import pandas as pd\n",
    "import glob\n",
    "\n",
    "!mkdir biosample_sra\n",
    "\n",
    "biosample = pd.DataFrame(columns=[\n",
    "    'replicate','description','*geo_loc_name','*host',\n",
    "    '*collection_date','sample_title','*organism','*env_medium',\n",
    "    '*lat_lon','*env_broad_scale','*env_local_scale','source_site','treatment','time point','original_id'])\n",
    "\n",
    "biosample.index.name = '*sample_name'\n",
    "\n",
    "\n",
    "organism = 'epiphytic metagenome'\n",
    "host = 'Halophila stipulacea'\n",
    "environmental_medium = 'water'\n",
    "broad_scale_environmental_context = 'marine seagrass meadow'\n",
    "\n",
    "metadata = pd.read_csv('metadata/metadata.tsv',sep='\\t',index_col=0)\n",
    "metadata = metadata.loc[metadata.Fraction!='water']\n",
    "\n",
    "samples = [i.split('/')[-1].split('_')[0] for i in glob.glob('raw_reads/*.fastq.gz')]\n",
    "\n",
    "samples = set(samples)\n",
    "\n",
    "replicate = 'biological replicate %i'\n",
    "\n",
    "replicate_counter = {}\n",
    "\n",
    "description = 'Epiphytic metagenome sample from Halophila stipulacea in a mesocosm experiment. Source site %s, treatment %s'\n",
    "\n",
    "collection_dates = ['15-Aug-2019',0,0,'08-Sep-2019',0,'22-Sep-2019',0,0,'13-Oct-2019']\n",
    "\n",
    "for smpl in samples:\n",
    "    if smpl not in metadata.index.tolist():\n",
    "        continue\n",
    "        \n",
    "    if smpl not in table.index.tolist():\n",
    "        continue\n",
    "        \n",
    "    geo_loc_name = 'Israel:Hatzeva,DeadSeaAndAravaScienceCenter'\n",
    "    lat_lon = '30.77 N 35.24 E'\n",
    "    local_scale_environmental_context = \"mesocosm experiment\"\n",
    "    try:\n",
    "        collection_date = collection_dates[int(metadata.at[smpl,'TP'])]\n",
    "    except:\n",
    "        collection_date = '15-Dec-2019'\n",
    "    timepoint = metadata.at[smpl,'TP']\n",
    "    source_site = metadata.at[smpl,'SourceSite']\n",
    "    treatment = metadata.at[smpl,'Treatment']\n",
    "    try:\n",
    "        description = 'Epiphytic metagenome sample from Halophila stipulacea in a mesocosm experiment. Source site %s, treatment %s, T%i' % (source_site,treatment,timepoint)\n",
    "    except:\n",
    "        timepoint = 0\n",
    "    if metadata.at[smpl,'Fraction'] == 'Field' and metadata.at[smpl,'SourceSite'] == 'TY' :\n",
    "        geo_loc_name = 'Israel:Eilat,TurYamBeach'\n",
    "        lat_lon = '29.51 N 34.92 E'\n",
    "        local_scale_environmental_context = \"Gulf of Aqaba Halophila stipulacea meadow\"\n",
    "        description = 'Epiphytic metagenome sample of Halophila stipulacea from Tur Yam Beach, Eilat'\n",
    "    elif metadata.at[smpl,'Fraction'] == 'Field' and metadata.at[smpl,'SourceSite'] == 'SB' :\n",
    "        geo_loc_name = 'Israel:Eilat,SouthBeach'\n",
    "        lat_lon = '29.49 N 34.91 E'\n",
    "        local_scale_environmental_context = \"Gulf of Aqaba Halophila stipulacea meadow\"\n",
    "        description = 'Epiphytic metagenome sample of Halophila stipulacea from South Beach, Eilat'\n",
    "    \n",
    "    if description in replicate_counter:\n",
    "        replicate_counter[description] += 1\n",
    "    else:\n",
    "        replicate_counter[description] = 1\n",
    "        \n",
    "    rep = replicate%replicate_counter[description]\n",
    "    \n",
    "    \n",
    "    \n",
    "    \n",
    "    biosample.loc[smpl] = [\n",
    "                    rep,\n",
    "                    description +', '+ rep,\n",
    "                    geo_loc_name,\n",
    "                    host,\n",
    "                    collection_date,\n",
    "                    description +', '+ rep,\n",
    "                    organism,\n",
    "                    environmental_medium,\n",
    "                    lat_lon,\n",
    "                    broad_scale_environmental_context,\n",
    "                    local_scale_environmental_context,\n",
    "                    source_site,\n",
    "                    treatment,\n",
    "                    timepoint,smpl]\n",
    "            \n",
    "for smpl in samples:\n",
    "    if smpl not in biosample.index:\n",
    "        print(smpl)\n",
    "        \n",
    "biosample.to_csv('biosample_sra/BioSample_metadata_epiphytes.tsv',sep='\\t')\n",
    "biosample"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "mkdir: cannot create directory ‘biosample_sra’: File exists\n",
      "AS2003\n",
      "AS2067\n",
      "AS2103\n",
      "AS2011\n",
      "AS2076\n",
      "AS2120\n",
      "AS2114\n",
      "AS2214\n",
      "AS2053\n",
      "AS2202\n",
      "AS2033\n",
      "AS2084\n",
      "AS2004\n",
      "AS2140\n",
      "AS2082\n",
      "AS2110\n",
      "AS2086\n",
      "AS2080\n",
      "AS2128\n",
      "AS2057\n",
      "AS2029\n",
      "AS2127\n",
      "AS2050\n",
      "AS2055\n",
      "AS2010\n",
      "AS2116\n",
      "Tank-8B\n",
      "AS2136\n",
      "AS2016\n",
      "AS2083\n",
      "AS2087\n",
      "AS2045\n",
      "Tank-17A\n",
      "AS2139\n",
      "AS2130\n",
      "AS2024\n",
      "AS2025\n",
      "AS2135\n",
      "AS2143\n",
      "Tank-7D\n",
      "AS2126\n",
      "AS2093\n",
      "AS2201\n",
      "AS2064\n",
      "AS2119\n",
      "AS2092\n",
      "AS2081\n",
      "AS2200\n",
      "AS2124\n",
      "AS2146\n",
      "AS2035\n",
      "AS2100\n",
      "AS2158\n",
      "NTC-22\n",
      "AS2157\n",
      "AS2013\n",
      "AS2023\n",
      "AS2098\n",
      "Tank-7A\n",
      "AS2014\n",
      "AS2213\n",
      "AS2070\n",
      "AS2006\n",
      "AS2137\n",
      "AS2089\n",
      "AS2027\n",
      "AS2054\n",
      "AS2138\n",
      "AS2217\n",
      "AS2026\n",
      "AS2036\n",
      "AS2069\n",
      "AS2156\n",
      "AS2131\n",
      "AS2079\n",
      "Tank-17C\n",
      "AS2145\n",
      "AS2154\n",
      "AS2203\n",
      "AS2121\n",
      "AS2088\n",
      "AS2041\n",
      "AS2015\n",
      "AS2048\n",
      "AS2002\n",
      "AS2155\n",
      "AS2095\n",
      "AS2034\n",
      "AS2144\n",
      "AS2104\n",
      "AS2028\n",
      "AS2125\n",
      "AS2038\n",
      "AS2068\n",
      "AS2019\n",
      "AS2018\n",
      "AS2051\n",
      "AS2160\n",
      "AS2060\n",
      "Tank-13B\n",
      "AS2059\n",
      "AS2042\n",
      "AS2109\n",
      "AS2046\n",
      "AS2030\n",
      "AS2008\n",
      "AS2107\n",
      "AS2077\n",
      "Tank-16B\n",
      "AS2065\n",
      "AS2091\n",
      "AS2115\n",
      "AS2007\n",
      "AS2085\n",
      "AS2012\n",
      "AS2132\n",
      "AS2129\n",
      "AS2113\n",
      "AS2123\n",
      "Tank-12C\n",
      "AS2096\n",
      "NTC-PCR21\n",
      "AS2117\n",
      "AS2108\n",
      "AS2106\n",
      "AS2118\n",
      "AS2049\n",
      "AS2073\n",
      "NTC-PCR22\n",
      "AS2134\n",
      "AS2043\n",
      "AS2149\n",
      "AS2005\n",
      "AS2039\n",
      "AS2063\n",
      "AS2215\n",
      "AS2040\n",
      "AS2044\n",
      "AS2074\n",
      "AS2097\n",
      "NTC-21\n",
      "Tank-13C\n",
      "Tank-12A\n",
      "AS2056\n",
      "AS2066\n",
      "AS2212\n",
      "AS2094\n",
      "Tank-12D\n",
      "AS2047\n",
      "AS2001\n",
      "AS2078\n",
      "AS2099\n",
      "AS2122\n",
      "AS2009\n",
      "AS2150\n",
      "AS2020\n",
      "AS2153\n",
      "AS2105\n",
      "AS2133\n",
      "AS2147\n",
      "AS2037\n",
      "AS2205\n",
      "AS2148\n",
      "AS2058\n",
      "AS2159\n",
      "AS2017\n",
      "AS2052\n",
      "AS2075\n"
     ]
    },
    {
     "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>replicate</th>\n",
       "      <th>description</th>\n",
       "      <th>*geo_loc_name</th>\n",
       "      <th>*collection_date</th>\n",
       "      <th>sample_title</th>\n",
       "      <th>*organism</th>\n",
       "      <th>*env_medium</th>\n",
       "      <th>*lat_lon</th>\n",
       "      <th>*env_broad_scale</th>\n",
       "      <th>*env_local_scale</th>\n",
       "      <th>treatment</th>\n",
       "      <th>timepoint</th>\n",
       "      <th>original_id</th>\n",
       "      <th>depth</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>*sample_name</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>Tank-3B</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>08-Sep-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>CTCN</td>\n",
       "      <td>3.0</td>\n",
       "      <td>Tank-3B</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-7C</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>22-Sep-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>CTN</td>\n",
       "      <td>5.0</td>\n",
       "      <td>Tank-7C</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-8C</th>\n",
       "      <td>biological replicate 2</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>22-Sep-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>CTN</td>\n",
       "      <td>5.0</td>\n",
       "      <td>Tank-8C</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-2B</th>\n",
       "      <td>biological replicate 2</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>08-Sep-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>CTCN</td>\n",
       "      <td>3.0</td>\n",
       "      <td>Tank-2B</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-8A</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>15-Aug-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>CTN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>Tank-8A</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-17B</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>08-Sep-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>TN</td>\n",
       "      <td>3.0</td>\n",
       "      <td>Tank-17B</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-3D</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>13-Oct-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>CTCN</td>\n",
       "      <td>8.0</td>\n",
       "      <td>Tank-3D</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-2A</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>15-Aug-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>CTCN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>Tank-2A</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-16D</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>13-Oct-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>TN</td>\n",
       "      <td>8.0</td>\n",
       "      <td>Tank-16D</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-13D</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>13-Oct-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>TCN</td>\n",
       "      <td>8.0</td>\n",
       "      <td>Tank-13D</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-12B</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>08-Sep-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>TCN</td>\n",
       "      <td>3.0</td>\n",
       "      <td>Tank-12B</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-2D</th>\n",
       "      <td>biological replicate 2</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>13-Oct-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>CTCN</td>\n",
       "      <td>8.0</td>\n",
       "      <td>Tank-2D</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-16C</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>22-Sep-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>TN</td>\n",
       "      <td>5.0</td>\n",
       "      <td>Tank-16C</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-7B</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>08-Sep-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>CTN</td>\n",
       "      <td>3.0</td>\n",
       "      <td>Tank-7B</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-16A</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>15-Aug-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>TN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>Tank-16A</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-2C</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>22-Sep-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>CTCN</td>\n",
       "      <td>5.0</td>\n",
       "      <td>Tank-2C</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-17D</th>\n",
       "      <td>biological replicate 2</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>13-Oct-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>TN</td>\n",
       "      <td>8.0</td>\n",
       "      <td>Tank-17D</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-3C</th>\n",
       "      <td>biological replicate 2</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>22-Sep-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>CTCN</td>\n",
       "      <td>5.0</td>\n",
       "      <td>Tank-3C</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-13A</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>15-Aug-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>TCN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>Tank-13A</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-3A</th>\n",
       "      <td>biological replicate 2</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>15-Aug-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>CTCN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>Tank-3A</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tank-8D</th>\n",
       "      <td>biological replicate 1</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>Israel:Hatzeva,DeadSeaAndAravaScienceCenter</td>\n",
       "      <td>13-Oct-2019</td>\n",
       "      <td>Water metagenome from a Halophila stipulacea m...</td>\n",
       "      <td>water metagenome</td>\n",
       "      <td>artificial seawater</td>\n",
       "      <td>30.77 N 35.24 E</td>\n",
       "      <td>marine seagrass meadow</td>\n",
       "      <td>mesocosm experiment</td>\n",
       "      <td>CTN</td>\n",
       "      <td>8.0</td>\n",
       "      <td>Tank-8D</td>\n",
       "      <td>9m</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                           replicate  \\\n",
       "*sample_name                           \n",
       "Tank-3B       biological replicate 1   \n",
       "Tank-7C       biological replicate 1   \n",
       "Tank-8C       biological replicate 2   \n",
       "Tank-2B       biological replicate 2   \n",
       "Tank-8A       biological replicate 1   \n",
       "Tank-17B      biological replicate 1   \n",
       "Tank-3D       biological replicate 1   \n",
       "Tank-2A       biological replicate 1   \n",
       "Tank-16D      biological replicate 1   \n",
       "Tank-13D      biological replicate 1   \n",
       "Tank-12B      biological replicate 1   \n",
       "Tank-2D       biological replicate 2   \n",
       "Tank-16C      biological replicate 1   \n",
       "Tank-7B       biological replicate 1   \n",
       "Tank-16A      biological replicate 1   \n",
       "Tank-2C       biological replicate 1   \n",
       "Tank-17D      biological replicate 2   \n",
       "Tank-3C       biological replicate 2   \n",
       "Tank-13A      biological replicate 1   \n",
       "Tank-3A       biological replicate 2   \n",
       "Tank-8D       biological replicate 1   \n",
       "\n",
       "                                                    description  \\\n",
       "*sample_name                                                      \n",
       "Tank-3B       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-7C       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-8C       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-2B       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-8A       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-17B      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-3D       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-2A       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-16D      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-13D      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-12B      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-2D       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-16C      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-7B       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-16A      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-2C       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-17D      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-3C       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-13A      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-3A       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-8D       Water metagenome from a Halophila stipulacea m...   \n",
       "\n",
       "                                            *geo_loc_name *collection_date  \\\n",
       "*sample_name                                                                 \n",
       "Tank-3B       Israel:Hatzeva,DeadSeaAndAravaScienceCenter      08-Sep-2019   \n",
       "Tank-7C       Israel:Hatzeva,DeadSeaAndAravaScienceCenter      22-Sep-2019   \n",
       "Tank-8C       Israel:Hatzeva,DeadSeaAndAravaScienceCenter      22-Sep-2019   \n",
       "Tank-2B       Israel:Hatzeva,DeadSeaAndAravaScienceCenter      08-Sep-2019   \n",
       "Tank-8A       Israel:Hatzeva,DeadSeaAndAravaScienceCenter      15-Aug-2019   \n",
       "Tank-17B      Israel:Hatzeva,DeadSeaAndAravaScienceCenter      08-Sep-2019   \n",
       "Tank-3D       Israel:Hatzeva,DeadSeaAndAravaScienceCenter      13-Oct-2019   \n",
       "Tank-2A       Israel:Hatzeva,DeadSeaAndAravaScienceCenter      15-Aug-2019   \n",
       "Tank-16D      Israel:Hatzeva,DeadSeaAndAravaScienceCenter      13-Oct-2019   \n",
       "Tank-13D      Israel:Hatzeva,DeadSeaAndAravaScienceCenter      13-Oct-2019   \n",
       "Tank-12B      Israel:Hatzeva,DeadSeaAndAravaScienceCenter      08-Sep-2019   \n",
       "Tank-2D       Israel:Hatzeva,DeadSeaAndAravaScienceCenter      13-Oct-2019   \n",
       "Tank-16C      Israel:Hatzeva,DeadSeaAndAravaScienceCenter      22-Sep-2019   \n",
       "Tank-7B       Israel:Hatzeva,DeadSeaAndAravaScienceCenter      08-Sep-2019   \n",
       "Tank-16A      Israel:Hatzeva,DeadSeaAndAravaScienceCenter      15-Aug-2019   \n",
       "Tank-2C       Israel:Hatzeva,DeadSeaAndAravaScienceCenter      22-Sep-2019   \n",
       "Tank-17D      Israel:Hatzeva,DeadSeaAndAravaScienceCenter      13-Oct-2019   \n",
       "Tank-3C       Israel:Hatzeva,DeadSeaAndAravaScienceCenter      22-Sep-2019   \n",
       "Tank-13A      Israel:Hatzeva,DeadSeaAndAravaScienceCenter      15-Aug-2019   \n",
       "Tank-3A       Israel:Hatzeva,DeadSeaAndAravaScienceCenter      15-Aug-2019   \n",
       "Tank-8D       Israel:Hatzeva,DeadSeaAndAravaScienceCenter      13-Oct-2019   \n",
       "\n",
       "                                                   sample_title  \\\n",
       "*sample_name                                                      \n",
       "Tank-3B       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-7C       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-8C       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-2B       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-8A       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-17B      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-3D       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-2A       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-16D      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-13D      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-12B      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-2D       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-16C      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-7B       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-16A      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-2C       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-17D      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-3C       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-13A      Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-3A       Water metagenome from a Halophila stipulacea m...   \n",
       "Tank-8D       Water metagenome from a Halophila stipulacea m...   \n",
       "\n",
       "                     *organism          *env_medium         *lat_lon  \\\n",
       "*sample_name                                                           \n",
       "Tank-3B       water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-7C       water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-8C       water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-2B       water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-8A       water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-17B      water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-3D       water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-2A       water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-16D      water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-13D      water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-12B      water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-2D       water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-16C      water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-7B       water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-16A      water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-2C       water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-17D      water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-3C       water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-13A      water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-3A       water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "Tank-8D       water metagenome  artificial seawater  30.77 N 35.24 E   \n",
       "\n",
       "                    *env_broad_scale     *env_local_scale treatment  \\\n",
       "*sample_name                                                          \n",
       "Tank-3B       marine seagrass meadow  mesocosm experiment      CTCN   \n",
       "Tank-7C       marine seagrass meadow  mesocosm experiment       CTN   \n",
       "Tank-8C       marine seagrass meadow  mesocosm experiment       CTN   \n",
       "Tank-2B       marine seagrass meadow  mesocosm experiment      CTCN   \n",
       "Tank-8A       marine seagrass meadow  mesocosm experiment       CTN   \n",
       "Tank-17B      marine seagrass meadow  mesocosm experiment        TN   \n",
       "Tank-3D       marine seagrass meadow  mesocosm experiment      CTCN   \n",
       "Tank-2A       marine seagrass meadow  mesocosm experiment      CTCN   \n",
       "Tank-16D      marine seagrass meadow  mesocosm experiment        TN   \n",
       "Tank-13D      marine seagrass meadow  mesocosm experiment       TCN   \n",
       "Tank-12B      marine seagrass meadow  mesocosm experiment       TCN   \n",
       "Tank-2D       marine seagrass meadow  mesocosm experiment      CTCN   \n",
       "Tank-16C      marine seagrass meadow  mesocosm experiment        TN   \n",
       "Tank-7B       marine seagrass meadow  mesocosm experiment       CTN   \n",
       "Tank-16A      marine seagrass meadow  mesocosm experiment        TN   \n",
       "Tank-2C       marine seagrass meadow  mesocosm experiment      CTCN   \n",
       "Tank-17D      marine seagrass meadow  mesocosm experiment        TN   \n",
       "Tank-3C       marine seagrass meadow  mesocosm experiment      CTCN   \n",
       "Tank-13A      marine seagrass meadow  mesocosm experiment       TCN   \n",
       "Tank-3A       marine seagrass meadow  mesocosm experiment      CTCN   \n",
       "Tank-8D       marine seagrass meadow  mesocosm experiment       CTN   \n",
       "\n",
       "              timepoint original_id depth  \n",
       "*sample_name                               \n",
       "Tank-3B             3.0     Tank-3B    9m  \n",
       "Tank-7C             5.0     Tank-7C    9m  \n",
       "Tank-8C             5.0     Tank-8C    9m  \n",
       "Tank-2B             3.0     Tank-2B    9m  \n",
       "Tank-8A             0.0     Tank-8A    9m  \n",
       "Tank-17B            3.0    Tank-17B    9m  \n",
       "Tank-3D             8.0     Tank-3D    9m  \n",
       "Tank-2A             0.0     Tank-2A    9m  \n",
       "Tank-16D            8.0    Tank-16D    9m  \n",
       "Tank-13D            8.0    Tank-13D    9m  \n",
       "Tank-12B            3.0    Tank-12B    9m  \n",
       "Tank-2D             8.0     Tank-2D    9m  \n",
       "Tank-16C            5.0    Tank-16C    9m  \n",
       "Tank-7B             3.0     Tank-7B    9m  \n",
       "Tank-16A            0.0    Tank-16A    9m  \n",
       "Tank-2C             5.0     Tank-2C    9m  \n",
       "Tank-17D            8.0    Tank-17D    9m  \n",
       "Tank-3C             5.0     Tank-3C    9m  \n",
       "Tank-13A            0.0    Tank-13A    9m  \n",
       "Tank-3A             0.0     Tank-3A    9m  \n",
       "Tank-8D             8.0     Tank-8D    9m  "
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import pandas as pd\n",
    "import glob\n",
    "\n",
    "!mkdir biosample_sra\n",
    "\n",
    "biosample = pd.DataFrame(columns=[\n",
    "    'replicate','description','*geo_loc_name',\n",
    "    '*collection_date','sample_title','*organism','*env_medium',\n",
    "    '*lat_lon','*env_broad_scale','*env_local_scale','treatment','timepoint','original_id','depth'])\n",
    "\n",
    "biosample.index.name = '*sample_name'\n",
    "\n",
    "\n",
    "organism = 'water metagenome'\n",
    "environmental_medium = 'artificial seawater'\n",
    "broad_scale_environmental_context = 'marine seagrass meadow'\n",
    "\n",
    "metadata = pd.read_csv('metadata/metadata.tsv',sep='\\t',index_col=0)\n",
    "metadata = metadata.loc[metadata.Fraction=='water']\n",
    "\n",
    "samples = [i.split('/')[-1].split('_')[0] for i in glob.glob('raw_reads/*.fastq.gz')]\n",
    "\n",
    "samples = set(samples)\n",
    "\n",
    "replicate = 'biological replicate %i'\n",
    "\n",
    "replicate_counter = {}\n",
    "\n",
    "description = 'Water metagenome from a Halophila stipulacea mesocosm. Treatment %s, time point %s'\n",
    "\n",
    "collection_dates = ['15-Aug-2019',0,0,'08-Sep-2019',0,'22-Sep-2019',0,0,'13-Oct-2019']\n",
    "\n",
    "for smpl in samples:\n",
    "    if smpl not in metadata.index.tolist():\n",
    "        continue\n",
    "        \n",
    "    geo_loc_name = 'Israel:Hatzeva,DeadSeaAndAravaScienceCenter'\n",
    "    lat_lon = '30.77 N 35.24 E'\n",
    "    local_scale_environmental_context = \"mesocosm experiment\"\n",
    "    collection_date = collection_dates[int(metadata.at[smpl,'TP'])]\n",
    "    timepoint = metadata.at[smpl,'TP']\n",
    "    treatment = metadata.at[smpl,'Treatment']\n",
    "    desc = description % (treatment,timepoint)\n",
    "    \n",
    "    \n",
    "    if desc in replicate_counter:\n",
    "        replicate_counter[desc] += 1\n",
    "    else:\n",
    "        replicate_counter[desc] = 1\n",
    "        \n",
    "    rep = replicate%replicate_counter[desc]\n",
    "    \n",
    "    \n",
    "    \n",
    "    \n",
    "    biosample.loc[smpl] = [\n",
    "                    rep,\n",
    "                    desc +', '+ rep,\n",
    "                    geo_loc_name,\n",
    "                    collection_date,\n",
    "                    desc +', '+ rep,\n",
    "                    organism,\n",
    "                    environmental_medium,\n",
    "                    lat_lon,\n",
    "                    broad_scale_environmental_context,\n",
    "                    local_scale_environmental_context,\n",
    "                    treatment,\n",
    "                    timepoint,smpl,'9m']\n",
    "            \n",
    "for smpl in samples:\n",
    "    if smpl not in biosample.index:\n",
    "        print(smpl)\n",
    "        \n",
    "biosample.to_csv('biosample_sra/BioSample_metadata_water.tsv',sep='\\t')\n",
    "biosample"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [],
   "source": [
    "biosamples = pd.read_csv('biosample_sra/BioSample_metadata_epiphytes.tsv',sep='\\t',index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [],
   "source": [
    "import glob\n",
    "\n",
    "sra = pd.DataFrame(columns = [\n",
    "    'library_ID','title','library_strategy',\n",
    "    'library_source','library_selection','library_layout',\n",
    "    'platform','instrument_model','design_description',\n",
    "    'filetype','filename','filename2']\n",
    ")\n",
    "\n",
    "sra.index.name = 'sample_name'\n",
    "\n",
    "for smpl in biosamples.index:\n",
    "    biosample = smpl #sample_to_biosample[smpl]\n",
    "    library_ID = '%s' % smpl\n",
    "    title = biosamples.loc[biosamples.original_id==smpl]['description'].tolist()[0].replace('metagenome sample','16S-rRNA metabaecoding sequences')+' original ID %s' % biosample\n",
    "    library_strategy = 'AMPLICON'\n",
    "    library_source = 'GENOMIC'\n",
    "    library_selection = 'PCR'\n",
    "    library_layout = 'paired'\n",
    "    platform = 'ILLUMINA'\n",
    "    instrument_model = 'Illumina iSeq 100'\n",
    "    design_description = 'Single barcode, two-step PCR, V4 fragment'\n",
    "    filetype = 'fastq'\n",
    "    R1 = list(glob.glob('raw_reads/%s_*_*_R1_*.fastq.gz'%smpl))[0].split('/')[-1]\n",
    "    R2 = list(glob.glob('raw_reads/%s_*_*_R2_*.fastq.gz'%smpl))[0].split('/')[-1]\n",
    "    sra.loc[library_ID] = [biosample,title,library_strategy,library_source,\n",
    "                           library_selection,library_layout,platform,\n",
    "                           instrument_model,design_description,filetype,R1,R2]\n",
    "\n",
    "    \n",
    "    \n",
    "sra.to_csv('biosample_sra/sra_metadata_epiphytes.tsv',sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [],
   "source": [
    "biosamples = pd.read_csv('biosample_sra/BioSample_metadata_water.tsv',sep='\\t',index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [],
   "source": [
    "import glob\n",
    "\n",
    "sra = pd.DataFrame(columns = [\n",
    "    'library_ID','title','library_strategy',\n",
    "    'library_source','library_selection','library_layout',\n",
    "    'platform','instrument_model','design_description',\n",
    "    'filetype','filename','filename2']\n",
    ")\n",
    "\n",
    "sra.index.name = 'sample_name'\n",
    "\n",
    "for smpl in biosamples.index:\n",
    "    biosample = smpl #sample_to_biosample[smpl]\n",
    "    library_ID = '%s' % smpl\n",
    "    title = biosamples.loc[biosamples.original_id==smpl]['description'].tolist()[0].replace('metagenome sample','16S-rRNA metabaecoding sequences')+' original ID %s' % biosample\n",
    "    library_strategy = 'AMPLICON'\n",
    "    library_source = 'GENOMIC'\n",
    "    library_selection = 'PCR'\n",
    "    library_layout = 'paired'\n",
    "    platform = 'ILLUMINA'\n",
    "    instrument_model = 'Illumina iSeq 100'\n",
    "    design_description = 'Single barcode, two-step PCR, V4 fragment'\n",
    "    filetype = 'fastq'\n",
    "    R1 = list(glob.glob('raw_reads/%s_*_*_R1_*.fastq.gz'%smpl))[0].split('/')[-1]\n",
    "    R2 = list(glob.glob('raw_reads/%s_*_*_R2_*.fastq.gz'%smpl))[0].split('/')[-1]\n",
    "    sra.loc[library_ID] = [biosample,title,library_strategy,library_source,\n",
    "                           library_selection,library_layout,platform,\n",
    "                           instrument_model,design_description,filetype,R1,R2]\n",
    "\n",
    "    \n",
    "    \n",
    "sra.to_csv('biosample_sra/sra_metadata_water.tsv',sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [],
   "source": [
    "!mkdir temp\n",
    "\n",
    "for f in glob.glob('raw_reads/*.fastq.gz'):\n",
    "    for i in biosamples.index:\n",
    "        if '/%s_' % i in f:\n",
    "            n = f.replace('raw_reads','temp')\n",
    "            !cp $f $n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Comments on file upload\n",
    "1. put all the files in a single directory (do not zip or tar)\n",
    "\n",
    "2. cd to this directory \n",
    "\n",
    "3. `ftp -p -i`\n",
    "\n",
    "4. once inside ftp:\n",
    "\n",
    "`ftp> open ftp-private.ncbi.nlm.nih.gov`  \n",
    "`user from submission page`  \n",
    "`password from submission page`  \n",
    "`ftp> cd directory-from-submission-page`  \n",
    "`ftp> mkdir new_dir` \n",
    "`ftp> cd new_dir`  \n",
    "`ftp> mput *.fastq.gz`\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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