merge_sample_ASV_counts.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## This notebook lets you merge read counts of different samples based on their sample IDs. This can be useful if you have technical replicates that were sequenced separately and you want to use the sum of read counts to analyze your data."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Import all required modules"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import os as os"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Navigate to your working directory, which should contain both spreadsheets you want to merge"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "os.chdir(\"/Users/nastassia.patin/GitHub/MarineDNA/EMP-data\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Import the sheets you want to merge"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
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     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "a = pd.read_csv(\"EMP_marine_samples-18S.tsv\", sep='\\t')\n",
    "a.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
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       "\n",
       "[83 rows x 28623 columns]"
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = a.T\n",
    "df.columns = df.iloc[0]\n",
    "df = df.drop(df.index[0])\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
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       "13114.palenik.42.s015.135711         0         0         0         0   \n",
       "\n",
       "ASV ID                       ASV_28619 ASV_28620 ASV_28621 ASV_28622 ASV_28623  \n",
       "13114.palenik.42.s011.133263         0         0         0         0         0  \n",
       "13114.palenik.42.s011.135730         0         0         0         0         0  \n",
       "13114.palenik.42.s003.132607         0         0         0         0         0  \n",
       "13114.palenik.42.s003.132623         0         0         0         0         1  \n",
       "13114.palenik.42.s003.133263         0         0         0         0         0  \n",
       "...                                ...       ...       ...       ...       ...  \n",
       "13114.palenik.42.s006.133263         0         0         0         0         0  \n",
       "13114.palenik.42.s018.135711         0         0         0         0         0  \n",
       "13114.palenik.42.s018.133047         0         0         0         0         0  \n",
       "13114.palenik.42.s015.133263         0         0         0         0         0  \n",
       "13114.palenik.42.s015.135711         0         0         0         0         0  \n",
       "\n",
       "[83 rows x 28624 columns]"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df['new_index'] = df.index.to_series().str.split(\".\").str[:4].str.join(\".\")\n",
    "df = df[['new_index'] + [col for col in df.columns if col != 'new_index']]\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = df.groupby('new_index').sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    <tr style=\"text-align: right;\">\n",
       "      <th>new_index</th>\n",
       "      <th>13114.palenik.42.s001</th>\n",
       "      <th>13114.palenik.42.s002</th>\n",
       "      <th>13114.palenik.42.s003</th>\n",
       "      <th>13114.palenik.42.s004</th>\n",
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       "      <th>13114.palenik.42.s007</th>\n",
       "      <th>13114.palenik.42.s008</th>\n",
       "      <th>13114.palenik.42.s009</th>\n",
       "      <th>13114.palenik.42.s010</th>\n",
       "      <th>...</th>\n",
       "      <th>13114.tait.77.s002</th>\n",
       "      <th>13114.tait.77.s003</th>\n",
       "      <th>13114.tait.77.s004</th>\n",
       "      <th>13114.tait.77.s005</th>\n",
       "      <th>13114.tait.77.s006</th>\n",
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       "      <th>13114.tait.77.s008</th>\n",
       "      <th>13114.tait.77.s009</th>\n",
       "      <th>13114.zaneveld.9.s021</th>\n",
       "      <th>13114.zaneveld.9.s022</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ASV ID</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
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       "  <tbody>\n",
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       "      <th>ASV_1</th>\n",
       "      <td>2</td>\n",
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       "      <th>ASV_2</th>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <th>ASV_3</th>\n",
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       "    <tr>\n",
       "      <th>ASV_4</th>\n",
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       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ASV_5</th>\n",
       "      <td>1707</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ASV_28619</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ASV_28620</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>22</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ASV_28621</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ASV_28622</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ASV_28623</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>8</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>28623 rows × 39 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "new_index  13114.palenik.42.s001  13114.palenik.42.s002  \\\n",
       "ASV ID                                                    \n",
       "ASV_1                          2                      0   \n",
       "ASV_2                          0                      0   \n",
       "ASV_3                          0                      0   \n",
       "ASV_4                          0                      0   \n",
       "ASV_5                       1707                      0   \n",
       "...                          ...                    ...   \n",
       "ASV_28619                      0                      0   \n",
       "ASV_28620                      0                      0   \n",
       "ASV_28621                      0                      0   \n",
       "ASV_28622                      0                      0   \n",
       "ASV_28623                      0                      0   \n",
       "\n",
       "new_index  13114.palenik.42.s003  13114.palenik.42.s004  \\\n",
       "ASV ID                                                    \n",
       "ASV_1                          0                      0   \n",
       "ASV_2                          0                      9   \n",
       "ASV_3                          0                      0   \n",
       "ASV_4                          0                      0   \n",
       "ASV_5                          0                      0   \n",
       "...                          ...                    ...   \n",
       "ASV_28619                      0                      0   \n",
       "ASV_28620                      0                      0   \n",
       "ASV_28621                      0                      0   \n",
       "ASV_28622                      0                      0   \n",
       "ASV_28623                      1                      8   \n",
       "\n",
       "new_index  13114.palenik.42.s005  13114.palenik.42.s006  \\\n",
       "ASV ID                                                    \n",
       "ASV_1                          0                      0   \n",
       "ASV_2                          0                      0   \n",
       "ASV_3                          0                      0   \n",
       "ASV_4                          0                      0   \n",
       "ASV_5                          0                      0   \n",
       "...                          ...                    ...   \n",
       "ASV_28619                      0                      0   \n",
       "ASV_28620                      0                      0   \n",
       "ASV_28621                      0                      0   \n",
       "ASV_28622                      0                      0   \n",
       "ASV_28623                      0                      0   \n",
       "\n",
       "new_index  13114.palenik.42.s007  13114.palenik.42.s008  \\\n",
       "ASV ID                                                    \n",
       "ASV_1                          0                      0   \n",
       "ASV_2                          0                      0   \n",
       "ASV_3                          0                      0   \n",
       "ASV_4                          0                      0   \n",
       "ASV_5                          0                      0   \n",
       "...                          ...                    ...   \n",
       "ASV_28619                      0                      0   \n",
       "ASV_28620                      0                      0   \n",
       "ASV_28621                      0                      0   \n",
       "ASV_28622                      0                      0   \n",
       "ASV_28623                      0                      0   \n",
       "\n",
       "new_index  13114.palenik.42.s009  13114.palenik.42.s010  ...  \\\n",
       "ASV ID                                                   ...   \n",
       "ASV_1                          0                      0  ...   \n",
       "ASV_2                          0                      0  ...   \n",
       "ASV_3                          0                      0  ...   \n",
       "ASV_4                          0                      0  ...   \n",
       "ASV_5                          0                      0  ...   \n",
       "...                          ...                    ...  ...   \n",
       "ASV_28619                      0                      0  ...   \n",
       "ASV_28620                      0                      0  ...   \n",
       "ASV_28621                      0                      0  ...   \n",
       "ASV_28622                      0                      0  ...   \n",
       "ASV_28623                      0                      0  ...   \n",
       "\n",
       "new_index  13114.tait.77.s002  13114.tait.77.s003  13114.tait.77.s004  \\\n",
       "ASV ID                                                                  \n",
       "ASV_1                       0                   0                   0   \n",
       "ASV_2                       0                   0                   0   \n",
       "ASV_3                       0                   0                   0   \n",
       "ASV_4                       0                   0                   0   \n",
       "ASV_5                     297                   0                   0   \n",
       "...                       ...                 ...                 ...   \n",
       "ASV_28619                   0                   0                   0   \n",
       "ASV_28620                   0                   0                   0   \n",
       "ASV_28621                   0                   0                   0   \n",
       "ASV_28622                   0                   0                   0   \n",
       "ASV_28623                   0                   0                   0   \n",
       "\n",
       "new_index  13114.tait.77.s005  13114.tait.77.s006  13114.tait.77.s007  \\\n",
       "ASV ID                                                                  \n",
       "ASV_1                       0                   0                   0   \n",
       "ASV_2                       0                   0                   0   \n",
       "ASV_3                       0                   0                   0   \n",
       "ASV_4                       0                   0                   0   \n",
       "ASV_5                       0                   0                   0   \n",
       "...                       ...                 ...                 ...   \n",
       "ASV_28619                   0                   0                   0   \n",
       "ASV_28620                   0                   0                   0   \n",
       "ASV_28621                   0                   0                   0   \n",
       "ASV_28622                   0                   0                   0   \n",
       "ASV_28623                   0                   0                   0   \n",
       "\n",
       "new_index  13114.tait.77.s008  13114.tait.77.s009  13114.zaneveld.9.s021  \\\n",
       "ASV ID                                                                     \n",
       "ASV_1                       0                   0                      0   \n",
       "ASV_2                       0                   0                      0   \n",
       "ASV_3                       0                   0                      0   \n",
       "ASV_4                       0                   0                      0   \n",
       "ASV_5                       0                   0                      0   \n",
       "...                       ...                 ...                    ...   \n",
       "ASV_28619                   0                   0                      0   \n",
       "ASV_28620                   0                   0                     22   \n",
       "ASV_28621                   0                   0                      0   \n",
       "ASV_28622                   0                   0                      0   \n",
       "ASV_28623                   0                   0                      0   \n",
       "\n",
       "new_index  13114.zaneveld.9.s022  \n",
       "ASV ID                            \n",
       "ASV_1                          0  \n",
       "ASV_2                          0  \n",
       "ASV_3                          0  \n",
       "ASV_4                          0  \n",
       "ASV_5                          0  \n",
       "...                          ...  \n",
       "ASV_28619                      0  \n",
       "ASV_28620                      0  \n",
       "ASV_28621                      0  \n",
       "ASV_28622                      5  \n",
       "ASV_28623                      0  \n",
       "\n",
       "[28623 rows x 39 columns]"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_new = df.T\n",
    "df_new"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_new.to_csv(\"EMP_marine_samples-18S-samplesmerged.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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