Human_miR_sequences.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "06ae7dd0-3963-45f0-8dbc-c0df64f1403d",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import logomaker as lm\n",
    "import matplotlib.pyplot as plt\n",
    "import os\n",
    "import re"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "c6fa5116-8064-4799-adb5-bbd6d888e103",
   "metadata": {},
   "outputs": [],
   "source": [
    "current_dir=os.getcwd()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "24c6182e-e31a-4735-931b-cbf65a1e66be",
   "metadata": {},
   "outputs": [],
   "source": [
    "columns=[\"miR_name\", \"miR_ID\", \"pre-miRNA_sequences\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "3b9af64c-2ec9-4b37-b131-a0feed8c4298",
   "metadata": {},
   "outputs": [],
   "source": [
    "hsa_miR_sequence=pd.read_csv(f\"{current_dir}/Human_miR_sequences_fasta/hsa_miR_sequence.csv\",header=None, names=columns)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "8deeb6ef-07e6-49b6-b5f5-4540051325f7",
   "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>miR_name</th>\n",
       "      <th>miR_ID</th>\n",
       "      <th>pre-miRNA_sequences</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>hsa-let-7a-1</td>\n",
       "      <td>MI0000060</td>\n",
       "      <td>UGGGAUGAGGUAGUAGGUUGUAUAGUUUUAGGGUCACACCCACCAC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>hsa-let-7a-2</td>\n",
       "      <td>MI0000061</td>\n",
       "      <td>AGGUUGAGGUAGUAGGUUGUAUAGUUUAGAAUUACAUCAAGGGAGA...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>hsa-let-7a-3</td>\n",
       "      <td>MI0000062</td>\n",
       "      <td>GGGUGAGGUAGUAGGUUGUAUAGUUUGGGGCUCUGCCCUGCUAUGG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>hsa-let-7b</td>\n",
       "      <td>MI0000063</td>\n",
       "      <td>CGGGGUGAGGUAGUAGGUUGUGUGGUUUCAGGGCAGUGAUGUUGCC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>hsa-let-7c</td>\n",
       "      <td>MI0000064</td>\n",
       "      <td>GCAUCCGGGUUGAGGUAGUAGGUUGUAUGGUUUAGAGUUACACCCU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1912</th>\n",
       "      <td>hsa-mir-12132</td>\n",
       "      <td>MI0039734</td>\n",
       "      <td>UUAACAUCUUUUCCAUCAUAAUUCUCAUAGUAAUAAUAGUAAUGUU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1913</th>\n",
       "      <td>hsa-mir-12133</td>\n",
       "      <td>MI0039735</td>\n",
       "      <td>GAAGUGUACUUUUUAAUGGUGCCAAACAGCAGUUGAUCUAUAAUAA...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1914</th>\n",
       "      <td>hsa-mir-12135</td>\n",
       "      <td>MI0039739</td>\n",
       "      <td>UGUGGAUAUUCUUUUUUGAUACUACAGCAAAACUCAGCAAGUUGUA...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1915</th>\n",
       "      <td>hsa-mir-12136</td>\n",
       "      <td>MI0039740</td>\n",
       "      <td>GAAAAAGUCAUGGAGGCCAUGGGGUUGGCUUGAAACCAGCUUUGGG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1916</th>\n",
       "      <td>hsa-mir-9902-2</td>\n",
       "      <td>MI0041071</td>\n",
       "      <td>GCAGGGAAAGGGAACCCAGAAAUCUGGUAUGCCAGCAAAGAGAGUA...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1917 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            miR_name     miR_ID  \\\n",
       "0       hsa-let-7a-1  MI0000060   \n",
       "1       hsa-let-7a-2  MI0000061   \n",
       "2       hsa-let-7a-3  MI0000062   \n",
       "3         hsa-let-7b  MI0000063   \n",
       "4         hsa-let-7c  MI0000064   \n",
       "...              ...        ...   \n",
       "1912   hsa-mir-12132  MI0039734   \n",
       "1913   hsa-mir-12133  MI0039735   \n",
       "1914   hsa-mir-12135  MI0039739   \n",
       "1915   hsa-mir-12136  MI0039740   \n",
       "1916  hsa-mir-9902-2  MI0041071   \n",
       "\n",
       "                                    pre-miRNA_sequences  \n",
       "0     UGGGAUGAGGUAGUAGGUUGUAUAGUUUUAGGGUCACACCCACCAC...  \n",
       "1     AGGUUGAGGUAGUAGGUUGUAUAGUUUAGAAUUACAUCAAGGGAGA...  \n",
       "2     GGGUGAGGUAGUAGGUUGUAUAGUUUGGGGCUCUGCCCUGCUAUGG...  \n",
       "3     CGGGGUGAGGUAGUAGGUUGUGUGGUUUCAGGGCAGUGAUGUUGCC...  \n",
       "4     GCAUCCGGGUUGAGGUAGUAGGUUGUAUGGUUUAGAGUUACACCCU...  \n",
       "...                                                 ...  \n",
       "1912  UUAACAUCUUUUCCAUCAUAAUUCUCAUAGUAAUAAUAGUAAUGUU...  \n",
       "1913  GAAGUGUACUUUUUAAUGGUGCCAAACAGCAGUUGAUCUAUAAUAA...  \n",
       "1914  UGUGGAUAUUCUUUUUUGAUACUACAGCAAAACUCAGCAAGUUGUA...  \n",
       "1915  GAAAAAGUCAUGGAGGCCAUGGGGUUGGCUUGAAACCAGCUUUGGG...  \n",
       "1916  GCAGGGAAAGGGAACCCAGAAAUCUGGUAUGCCAGCAAAGAGAGUA...  \n",
       "\n",
       "[1917 rows x 3 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "hsa_miR_sequence"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "a583eeee-1815-49b4-b25f-592ea5c02f15",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "importing Jupyter notebook from EXONIC.ipynb\n"
     ]
    }
   ],
   "source": [
    "import import_ipynb\n",
    "from EXONIC import Regions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "c7b5625e-d2a1-4f72-b2f5-56d910ec7d4c",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_exonic_miR=Regions(f\"{current_dir}/Human_csv_file/human_exonic_miR(gene_type)_NCBI_unique.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "1178ea75-e186-4267-99f5-fae94561019b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['hostgene_chrom', 'hostgene_exonStarts', 'hostgene_exonEnds',\n",
       "       'hostgene_cdsStart', 'hostgene_cdsEnd', 'hostgene_strand',\n",
       "       'hostgene_exonCounts', 'hostgene_txStarts', 'hostgene_txEnds',\n",
       "       'pre_mRNA_length', 'mature_host_mRNA_Length', 'hostgene_Name',\n",
       "       'hostgene_NCBI_ID', 'miR_name', 'miR_chrom', 'miR_exonStarts',\n",
       "       'miR_exonEnds', 'miR_type', 'miR_strand', 'gene_type'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "human_exonic_miR.df.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "4309b930-dec1-461b-9d9b-762efe7dc8ee",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_exonic_miR.select([\"hostgene_NCBI_ID\",'hostgene_Name','hostgene_strand',\n",
    "                            'pre_mRNA_length','mature_host_mRNA_Length','miR_name','miR_strand', 'gene_type' ])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "dea6e045-2e2b-4572-8dcd-45d8c8b3c0b1",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\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>hostgene_NCBI_ID</th>\n",
       "      <th>hostgene_Name</th>\n",
       "      <th>hostgene_strand</th>\n",
       "      <th>pre_mRNA_length</th>\n",
       "      <th>mature_host_mRNA_Length</th>\n",
       "      <th>miR_name</th>\n",
       "      <th>miR_strand</th>\n",
       "      <th>gene_type</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>XM_047427799.1</td>\n",
       "      <td>COP1</td>\n",
       "      <td>-</td>\n",
       "      <td>209014.0</td>\n",
       "      <td>19460</td>\n",
       "      <td>hsa-mir-1843</td>\n",
       "      <td>-</td>\n",
       "      <td>protein-coding gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>NR_132742.1</td>\n",
       "      <td>MIR34AHG</td>\n",
       "      <td>-</td>\n",
       "      <td>34328.0</td>\n",
       "      <td>4157</td>\n",
       "      <td>hsa-mir-34a</td>\n",
       "      <td>-</td>\n",
       "      <td>non-coding gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NR_046105.1</td>\n",
       "      <td>MIR137HG</td>\n",
       "      <td>-</td>\n",
       "      <td>61694.0</td>\n",
       "      <td>2469</td>\n",
       "      <td>hsa-mir-137</td>\n",
       "      <td>-</td>\n",
       "      <td>non-coding gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>XM_047437906.1</td>\n",
       "      <td>LOC124904228</td>\n",
       "      <td>-</td>\n",
       "      <td>4590.0</td>\n",
       "      <td>4590</td>\n",
       "      <td>hsa-mir-2682</td>\n",
       "      <td>-</td>\n",
       "      <td>protein-coding gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>NM_006496.4</td>\n",
       "      <td>GNAI3</td>\n",
       "      <td>+</td>\n",
       "      <td>51581.0</td>\n",
       "      <td>9044</td>\n",
       "      <td>hsa-mir-197</td>\n",
       "      <td>+</td>\n",
       "      <td>protein-coding gene</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>196</th>\n",
       "      <td>NM_052945.4</td>\n",
       "      <td>TNFRSF13C</td>\n",
       "      <td>-</td>\n",
       "      <td>4775.0</td>\n",
       "      <td>3923</td>\n",
       "      <td>hsa-mir-378i</td>\n",
       "      <td>-</td>\n",
       "      <td>protein-coding gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>197</th>\n",
       "      <td>XM_047441696.1</td>\n",
       "      <td>LOC124905135</td>\n",
       "      <td>+</td>\n",
       "      <td>69285.0</td>\n",
       "      <td>16367</td>\n",
       "      <td>hsa-let-7a-3</td>\n",
       "      <td>+</td>\n",
       "      <td>protein-coding gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>198</th>\n",
       "      <td>XM_047441696.1</td>\n",
       "      <td>LOC124905135</td>\n",
       "      <td>+</td>\n",
       "      <td>69285.0</td>\n",
       "      <td>16367</td>\n",
       "      <td>hsa-mir-4763</td>\n",
       "      <td>+</td>\n",
       "      <td>protein-coding gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>199</th>\n",
       "      <td>XM_047441696.1</td>\n",
       "      <td>LOC124905135</td>\n",
       "      <td>+</td>\n",
       "      <td>69285.0</td>\n",
       "      <td>16367</td>\n",
       "      <td>hsa-let-7b</td>\n",
       "      <td>+</td>\n",
       "      <td>protein-coding gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>200</th>\n",
       "      <td>XR_002958733.2</td>\n",
       "      <td>LOC112268288</td>\n",
       "      <td>+</td>\n",
       "      <td>11753.0</td>\n",
       "      <td>11634</td>\n",
       "      <td>hsa-mir-3619</td>\n",
       "      <td>+</td>\n",
       "      <td>non-coding gene</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>201 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    hostgene_NCBI_ID hostgene_Name hostgene_strand  pre_mRNA_length  \\\n",
       "0     XM_047427799.1          COP1               -         209014.0   \n",
       "1        NR_132742.1      MIR34AHG               -          34328.0   \n",
       "2        NR_046105.1      MIR137HG               -          61694.0   \n",
       "3     XM_047437906.1  LOC124904228               -           4590.0   \n",
       "4        NM_006496.4         GNAI3               +          51581.0   \n",
       "..               ...           ...             ...              ...   \n",
       "196      NM_052945.4     TNFRSF13C               -           4775.0   \n",
       "197   XM_047441696.1  LOC124905135               +          69285.0   \n",
       "198   XM_047441696.1  LOC124905135               +          69285.0   \n",
       "199   XM_047441696.1  LOC124905135               +          69285.0   \n",
       "200   XR_002958733.2  LOC112268288               +          11753.0   \n",
       "\n",
       "     mature_host_mRNA_Length      miR_name miR_strand            gene_type  \n",
       "0                      19460  hsa-mir-1843          -  protein-coding gene  \n",
       "1                       4157   hsa-mir-34a          -      non-coding gene  \n",
       "2                       2469   hsa-mir-137          -      non-coding gene  \n",
       "3                       4590  hsa-mir-2682          -  protein-coding gene  \n",
       "4                       9044   hsa-mir-197          +  protein-coding gene  \n",
       "..                       ...           ...        ...                  ...  \n",
       "196                     3923  hsa-mir-378i          -  protein-coding gene  \n",
       "197                    16367  hsa-let-7a-3          +  protein-coding gene  \n",
       "198                    16367  hsa-mir-4763          +  protein-coding gene  \n",
       "199                    16367    hsa-let-7b          +  protein-coding gene  \n",
       "200                    11634  hsa-mir-3619          +      non-coding gene  \n",
       "\n",
       "[201 rows x 8 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "human_exonic_miR.df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "91af7dab",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_exonic_miR_sequence=human_exonic_miR.df.merge(hsa_miR_sequence, on=\"miR_name\",how=\"inner\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "4ed1ab13",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_exonic_miR_sequence.drop(columns=[\"miR_ID\"], inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "4dcf193a",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_exonic_miR_sequence.to_excel(f\"{current_dir}/Human_miR_sequences_fasta/Human_exonic_miR_sequence_unique.xlsx\",index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "12a5f3eb",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_exonic_miR_sequence.to_csv(f\"{current_dir}/Human_miR_sequences_fasta/Human_exonic_miR_sequence_unique.csv\",index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "76b4f777",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>hostgene_NCBI_ID</th>\n",
       "      <th>hostgene_Name</th>\n",
       "      <th>hostgene_strand</th>\n",
       "      <th>pre_mRNA_length</th>\n",
       "      <th>mature_host_mRNA_Length</th>\n",
       "      <th>miR_name</th>\n",
       "      <th>miR_strand</th>\n",
       "      <th>gene_type</th>\n",
       "      <th>pre-miRNA_sequences</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>XM_047427799.1</td>\n",
       "      <td>COP1</td>\n",
       "      <td>-</td>\n",
       "      <td>209014.0</td>\n",
       "      <td>19460</td>\n",
       "      <td>hsa-mir-1843</td>\n",
       "      <td>-</td>\n",
       "      <td>protein-coding gene</td>\n",
       "      <td>GCAGCGAUCCUACAUAAAUAUAUGGAGGUCUCUGUCUGGCUUAGGA...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>NR_132742.1</td>\n",
       "      <td>MIR34AHG</td>\n",
       "      <td>-</td>\n",
       "      <td>34328.0</td>\n",
       "      <td>4157</td>\n",
       "      <td>hsa-mir-34a</td>\n",
       "      <td>-</td>\n",
       "      <td>non-coding gene</td>\n",
       "      <td>GGCCAGCUGUGAGUGUUUCUUUGGCAGUGUCUUAGCUGGUUGUUGU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NR_046105.1</td>\n",
       "      <td>MIR137HG</td>\n",
       "      <td>-</td>\n",
       "      <td>61694.0</td>\n",
       "      <td>2469</td>\n",
       "      <td>hsa-mir-137</td>\n",
       "      <td>-</td>\n",
       "      <td>non-coding gene</td>\n",
       "      <td>GGUCCUCUGACUCUCUUCGGUGACGGGUAUUCUUGGGUGGAUAAUA...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>XM_047437906.1</td>\n",
       "      <td>LOC124904228</td>\n",
       "      <td>-</td>\n",
       "      <td>4590.0</td>\n",
       "      <td>4590</td>\n",
       "      <td>hsa-mir-2682</td>\n",
       "      <td>-</td>\n",
       "      <td>protein-coding gene</td>\n",
       "      <td>ACCUUCCUGAAAGAGGUUGGGGCAGGCAGUGACUGUUCAGACGUCC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>NM_006496.4</td>\n",
       "      <td>GNAI3</td>\n",
       "      <td>+</td>\n",
       "      <td>51581.0</td>\n",
       "      <td>9044</td>\n",
       "      <td>hsa-mir-197</td>\n",
       "      <td>+</td>\n",
       "      <td>protein-coding gene</td>\n",
       "      <td>GGCUGUGCCGGGUAGAGAGGGCAGUGGGAGGUAAGAGCUCUUCACC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>196</th>\n",
       "      <td>NM_052945.4</td>\n",
       "      <td>TNFRSF13C</td>\n",
       "      <td>-</td>\n",
       "      <td>4775.0</td>\n",
       "      <td>3923</td>\n",
       "      <td>hsa-mir-378i</td>\n",
       "      <td>-</td>\n",
       "      <td>protein-coding gene</td>\n",
       "      <td>GGGAGCACUGGACUAGGAGUCAGAAGGUGGAGUUCUGGGUGCUGUU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>197</th>\n",
       "      <td>XM_047441696.1</td>\n",
       "      <td>LOC124905135</td>\n",
       "      <td>+</td>\n",
       "      <td>69285.0</td>\n",
       "      <td>16367</td>\n",
       "      <td>hsa-let-7a-3</td>\n",
       "      <td>+</td>\n",
       "      <td>protein-coding gene</td>\n",
       "      <td>GGGUGAGGUAGUAGGUUGUAUAGUUUGGGGCUCUGCCCUGCUAUGG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>198</th>\n",
       "      <td>XM_047441696.1</td>\n",
       "      <td>LOC124905135</td>\n",
       "      <td>+</td>\n",
       "      <td>69285.0</td>\n",
       "      <td>16367</td>\n",
       "      <td>hsa-mir-4763</td>\n",
       "      <td>+</td>\n",
       "      <td>protein-coding gene</td>\n",
       "      <td>CCUGUCCCUCCUGCCCUGCGCCUGCCCAGCCCUCCUGCUCUGGUGA...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>199</th>\n",
       "      <td>XM_047441696.1</td>\n",
       "      <td>LOC124905135</td>\n",
       "      <td>+</td>\n",
       "      <td>69285.0</td>\n",
       "      <td>16367</td>\n",
       "      <td>hsa-let-7b</td>\n",
       "      <td>+</td>\n",
       "      <td>protein-coding gene</td>\n",
       "      <td>CGGGGUGAGGUAGUAGGUUGUGUGGUUUCAGGGCAGUGAUGUUGCC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>200</th>\n",
       "      <td>XR_002958733.2</td>\n",
       "      <td>LOC112268288</td>\n",
       "      <td>+</td>\n",
       "      <td>11753.0</td>\n",
       "      <td>11634</td>\n",
       "      <td>hsa-mir-3619</td>\n",
       "      <td>+</td>\n",
       "      <td>non-coding gene</td>\n",
       "      <td>ACGGCAUCUUUGCACUCAGCAGGCAGGCUGGUGCAGCCCGUGGUGG...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>201 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    hostgene_NCBI_ID hostgene_Name hostgene_strand  pre_mRNA_length  \\\n",
       "0     XM_047427799.1          COP1               -         209014.0   \n",
       "1        NR_132742.1      MIR34AHG               -          34328.0   \n",
       "2        NR_046105.1      MIR137HG               -          61694.0   \n",
       "3     XM_047437906.1  LOC124904228               -           4590.0   \n",
       "4        NM_006496.4         GNAI3               +          51581.0   \n",
       "..               ...           ...             ...              ...   \n",
       "196      NM_052945.4     TNFRSF13C               -           4775.0   \n",
       "197   XM_047441696.1  LOC124905135               +          69285.0   \n",
       "198   XM_047441696.1  LOC124905135               +          69285.0   \n",
       "199   XM_047441696.1  LOC124905135               +          69285.0   \n",
       "200   XR_002958733.2  LOC112268288               +          11753.0   \n",
       "\n",
       "     mature_host_mRNA_Length      miR_name miR_strand            gene_type  \\\n",
       "0                      19460  hsa-mir-1843          -  protein-coding gene   \n",
       "1                       4157   hsa-mir-34a          -      non-coding gene   \n",
       "2                       2469   hsa-mir-137          -      non-coding gene   \n",
       "3                       4590  hsa-mir-2682          -  protein-coding gene   \n",
       "4                       9044   hsa-mir-197          +  protein-coding gene   \n",
       "..                       ...           ...        ...                  ...   \n",
       "196                     3923  hsa-mir-378i          -  protein-coding gene   \n",
       "197                    16367  hsa-let-7a-3          +  protein-coding gene   \n",
       "198                    16367  hsa-mir-4763          +  protein-coding gene   \n",
       "199                    16367    hsa-let-7b          +  protein-coding gene   \n",
       "200                    11634  hsa-mir-3619          +      non-coding gene   \n",
       "\n",
       "                                   pre-miRNA_sequences  \n",
       "0    GCAGCGAUCCUACAUAAAUAUAUGGAGGUCUCUGUCUGGCUUAGGA...  \n",
       "1    GGCCAGCUGUGAGUGUUUCUUUGGCAGUGUCUUAGCUGGUUGUUGU...  \n",
       "2    GGUCCUCUGACUCUCUUCGGUGACGGGUAUUCUUGGGUGGAUAAUA...  \n",
       "3    ACCUUCCUGAAAGAGGUUGGGGCAGGCAGUGACUGUUCAGACGUCC...  \n",
       "4    GGCUGUGCCGGGUAGAGAGGGCAGUGGGAGGUAAGAGCUCUUCACC...  \n",
       "..                                                 ...  \n",
       "196  GGGAGCACUGGACUAGGAGUCAGAAGGUGGAGUUCUGGGUGCUGUU...  \n",
       "197  GGGUGAGGUAGUAGGUUGUAUAGUUUGGGGCUCUGCCCUGCUAUGG...  \n",
       "198  CCUGUCCCUCCUGCCCUGCGCCUGCCCAGCCCUCCUGCUCUGGUGA...  \n",
       "199  CGGGGUGAGGUAGUAGGUUGUGUGGUUUCAGGGCAGUGAUGUUGCC...  \n",
       "200  ACGGCAUCUUUGCACUCAGCAGGCAGGCUGGUGCAGCCCGUGGUGG...  \n",
       "\n",
       "[201 rows x 9 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "human_exonic_miR_sequence"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "67e854d8",
   "metadata": {},
   "source": [
    "### protein-coding host genes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "7e50789d",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_exonic_protein_coding_miR=Regions(f\"{current_dir}/Human_csv_file/human_exonic_miR_list(protein_coding_host_genes)_NCBI_unique.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "da95a8bb",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_exonic_protein_coding_miR.select(['hostgene_NCBI_ID', 'hostgene_Name', 'hostgene_strand',\n",
    "       'miR_name', 'miR_strand', 'region','pre_mRNA_length', 'mature_host_mRNA_Length', 'gene_type'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "bf8a4ba1",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_exonic_miR_sequence_coding=human_exonic_protein_coding_miR.df.merge(hsa_miR_sequence, on=\"miR_name\",how=\"inner\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "50ef4571",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_exonic_miR_sequence_coding.drop(columns=[\"miR_ID\"], inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "00f67184",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_exonic_miR_sequence_coding.to_csv(f\"{current_dir}/Human_miR_sequences_fasta/Human_exonic_miR_sequence_protein_coding_unique.csv\",index=False)\n",
    "human_exonic_miR_sequence_coding.to_excel(f\"{current_dir}/Human_miR_sequences_fasta/Human_exonic_miR_sequence_protein_coding_unique.xlsx\",index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a914e47d",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "0034631a",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "9ef8bd55",
   "metadata": {},
   "source": [
    "### Mature miRNA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "c431dfab",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_exonic_miR_sequence_forfasta=Regions(f\"{current_dir}/Human_miR_sequences_fasta/Human_exonic_miR_sequence_unique.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "d0e13d9b",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_exonic_miR_sequence_forfasta.select(['miR_name','pre-miRNA_sequences'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "83386eb8-1f7e-4882-be12-2d967a24164e",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_exonic_miR_sequence_forfasta.df.to_csv(f\"{current_dir}/Human_miR_sequences_fasta/Human_exonic_miR_sequence_forfasta.csv\",index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "8531143a-89cc-4cc8-adaf-3b9a9bb56f69",
   "metadata": {},
   "outputs": [],
   "source": [
    "mature_columns=[\"miR_mature_name\",\"miR_ID\",\"genus\", \"species\",\"miR_name2\",\"mature_miR_sequences\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "68f580ac-ec26-4eba-a59e-101a39d4ed11",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_mature_miR=pd.read_csv(f\"{current_dir}/mature_miR/mature_miR.csv\",header=None, names=mature_columns)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "d2b3a119-8a16-41a6-8707-162eeaf3a72a",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_mature_miR.drop(columns=[\"miR_ID\",\"genus\", \"species\",\"miR_name2\"],inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "9007aae1-7f66-4528-9238-5e023be11385",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "    }\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>miR_mature_name</th>\n",
       "      <th>mature_miR_sequences</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>cel-let-7-5p</td>\n",
       "      <td>UGAGGUAGUAGGUUGUAUAGUU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>cel-let-7-3p</td>\n",
       "      <td>CUAUGCAAUUUUCUACCUUACC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>cel-lin-4-5p</td>\n",
       "      <td>UCCCUGAGACCUCAAGUGUGA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>cel-lin-4-3p</td>\n",
       "      <td>ACACCUGGGCUCUCCGGGUACC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>cel-miR-1-5p</td>\n",
       "      <td>CAUACUUCCUUACAUGCCCAUA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48880</th>\n",
       "      <td>smc-miR-12461-3p</td>\n",
       "      <td>AGUAAAUGAUCAGCAUCCUCCA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48881</th>\n",
       "      <td>gga-miR-1784b-5p</td>\n",
       "      <td>UUCUGCUCCUAUUUAAGUCAAU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48882</th>\n",
       "      <td>gga-miR-1784b-3p</td>\n",
       "      <td>UGAUUUCAAUAAGAGCAGAAUU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48883</th>\n",
       "      <td>mdo-miR-7385g-3p</td>\n",
       "      <td>AGCAUAGAAUGUCAGAUCUAG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48884</th>\n",
       "      <td>mdo-miR-7385g-2-3p</td>\n",
       "      <td>AGCAUAGAAUGUCAGGUCUAG</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>48885 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          miR_mature_name    mature_miR_sequences\n",
       "0            cel-let-7-5p  UGAGGUAGUAGGUUGUAUAGUU\n",
       "1            cel-let-7-3p  CUAUGCAAUUUUCUACCUUACC\n",
       "2            cel-lin-4-5p   UCCCUGAGACCUCAAGUGUGA\n",
       "3            cel-lin-4-3p  ACACCUGGGCUCUCCGGGUACC\n",
       "4            cel-miR-1-5p  CAUACUUCCUUACAUGCCCAUA\n",
       "...                   ...                     ...\n",
       "48880    smc-miR-12461-3p  AGUAAAUGAUCAGCAUCCUCCA\n",
       "48881    gga-miR-1784b-5p  UUCUGCUCCUAUUUAAGUCAAU\n",
       "48882    gga-miR-1784b-3p  UGAUUUCAAUAAGAGCAGAAUU\n",
       "48883    mdo-miR-7385g-3p   AGCAUAGAAUGUCAGAUCUAG\n",
       "48884  mdo-miR-7385g-2-3p   AGCAUAGAAUGUCAGGUCUAG\n",
       "\n",
       "[48885 rows x 2 columns]"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "human_mature_miR"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "6e086d20-970c-46f8-bfb0-80571aefd7ac",
   "metadata": {},
   "outputs": [],
   "source": [
    "human_mature_miR = human_mature_miR.loc[human_mature_miR['miR_mature_name'].str.contains(r'^hsa-', flags=re.I, regex=True)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "7cf82bec-0683-4ac2-ac2e-69a31329b04a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>miR_mature_name</th>\n",
       "      <th>mature_miR_sequences</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>112</th>\n",
       "      <td>hsa-let-7a-5p</td>\n",
       "      <td>UGAGGUAGUAGGUUGUAUAGUU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>113</th>\n",
       "      <td>hsa-let-7a-3p</td>\n",
       "      <td>CUAUACAAUCUACUGUCUUUC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>114</th>\n",
       "      <td>hsa-let-7a-2-3p</td>\n",
       "      <td>CUGUACAGCCUCCUAGCUUUCC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>115</th>\n",
       "      <td>hsa-let-7b-5p</td>\n",
       "      <td>UGAGGUAGUAGGUUGUGUGGUU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>116</th>\n",
       "      <td>hsa-let-7b-3p</td>\n",
       "      <td>CUAUACAACCUACUGCCUUCCC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47417</th>\n",
       "      <td>hsa-miR-12131</td>\n",
       "      <td>UUUGGAGAGGUGUACUCCCA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47418</th>\n",
       "      <td>hsa-miR-12132</td>\n",
       "      <td>UAUUACUGUGAGAAUUAUGAUG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47419</th>\n",
       "      <td>hsa-miR-12133</td>\n",
       "      <td>CUUGGCACCAUUAAAAAGUACA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47423</th>\n",
       "      <td>hsa-miR-12135</td>\n",
       "      <td>UAAAGGUUUGUUUGUAAA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47424</th>\n",
       "      <td>hsa-miR-12136</td>\n",
       "      <td>GAAAAAGUCAUGGAGGCC</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2656 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       miR_mature_name    mature_miR_sequences\n",
       "112      hsa-let-7a-5p  UGAGGUAGUAGGUUGUAUAGUU\n",
       "113      hsa-let-7a-3p   CUAUACAAUCUACUGUCUUUC\n",
       "114    hsa-let-7a-2-3p  CUGUACAGCCUCCUAGCUUUCC\n",
       "115      hsa-let-7b-5p  UGAGGUAGUAGGUUGUGUGGUU\n",
       "116      hsa-let-7b-3p  CUAUACAACCUACUGCCUUCCC\n",
       "...                ...                     ...\n",
       "47417    hsa-miR-12131    UUUGGAGAGGUGUACUCCCA\n",
       "47418    hsa-miR-12132  UAUUACUGUGAGAAUUAUGAUG\n",
       "47419    hsa-miR-12133  CUUGGCACCAUUAAAAAGUACA\n",
       "47423    hsa-miR-12135      UAAAGGUUUGUUUGUAAA\n",
       "47424    hsa-miR-12136      GAAAAAGUCAUGGAGGCC\n",
       "\n",
       "[2656 rows x 2 columns]"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "human_mature_miR"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "b84390c0-fbd7-47c1-a9d4-621f0241e933",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/var/folders/hc/mc3kqq154077vn1n8slj6jsr0000gr/T/ipykernel_14857/1365459275.py:10: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  human_mature_miR['standard_id'] = human_mature_miR['miR_mature_name'].apply(extract_id)\n"
     ]
    }
   ],
   "source": [
    "# Function to extract the relevant part from the identifier\n",
    "def extract_id(identifier):\n",
    "    match = re.search(r'(\\d+[a-zA-Z]?)', identifier)\n",
    "    return match.group(0) if match else None\n",
    "\n",
    "# Standardize identifiers in df1\n",
    "human_exonic_miR_sequence['standard_id'] = human_exonic_miR_sequence['miR_name'].apply(extract_id)\n",
    "\n",
    "# Standardize identifiers in df2\n",
    "human_mature_miR['standard_id'] = human_mature_miR['miR_mature_name'].apply(extract_id)\n",
    "\n",
    "# Merge the dataframes on the standardized identifiers\n",
    "merged_df = pd.merge(human_exonic_miR_sequence, human_mature_miR, on='standard_id', how='inner')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "4aaa685f-19fa-45f1-8240-08fe3a97e5b8",
   "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>hostgene_NCBI_ID</th>\n",
       "      <th>hostgene_Name</th>\n",
       "      <th>hostgene_strand</th>\n",
       "      <th>pre_mRNA_length</th>\n",
       "      <th>mature_host_mRNA_Length</th>\n",
       "      <th>miR_name</th>\n",
       "      <th>miR_strand</th>\n",
       "      <th>gene_type</th>\n",
       "      <th>pre-miRNA_sequences</th>\n",
       "      <th>standard_id</th>\n",
       "      <th>miR_mature_name</th>\n",
       "      <th>mature_miR_sequences</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>XM_047427799.1</td>\n",
       "      <td>COP1</td>\n",
       "      <td>-</td>\n",
       "      <td>209014.0</td>\n",
       "      <td>19460</td>\n",
       "      <td>hsa-mir-1843</td>\n",
       "      <td>-</td>\n",
       "      <td>protein-coding gene</td>\n",
       "      <td>GCAGCGAUCCUACAUAAAUAUAUGGAGGUCUCUGUCUGGCUUAGGA...</td>\n",
       "      <td>1843</td>\n",
       "      <td>hsa-miR-1843</td>\n",
       "      <td>UAUGGAGGUCUCUGUCUGGC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>NR_132742.1</td>\n",
       "      <td>MIR34AHG</td>\n",
       "      <td>-</td>\n",
       "      <td>34328.0</td>\n",
       "      <td>4157</td>\n",
       "      <td>hsa-mir-34a</td>\n",
       "      <td>-</td>\n",
       "      <td>non-coding gene</td>\n",
       "      <td>GGCCAGCUGUGAGUGUUUCUUUGGCAGUGUCUUAGCUGGUUGUUGU...</td>\n",
       "      <td>34a</td>\n",
       "      <td>hsa-miR-34a-5p</td>\n",
       "      <td>UGGCAGUGUCUUAGCUGGUUGU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NR_132742.1</td>\n",
       "      <td>MIR34AHG</td>\n",
       "      <td>-</td>\n",
       "      <td>34328.0</td>\n",
       "      <td>4157</td>\n",
       "      <td>hsa-mir-34a</td>\n",
       "      <td>-</td>\n",
       "      <td>non-coding gene</td>\n",
       "      <td>GGCCAGCUGUGAGUGUUUCUUUGGCAGUGUCUUAGCUGGUUGUUGU...</td>\n",
       "      <td>34a</td>\n",
       "      <td>hsa-miR-34a-3p</td>\n",
       "      <td>CAAUCAGCAAGUAUACUGCCCU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>NR_046105.1</td>\n",
       "      <td>MIR137HG</td>\n",
       "      <td>-</td>\n",
       "      <td>61694.0</td>\n",
       "      <td>2469</td>\n",
       "      <td>hsa-mir-137</td>\n",
       "      <td>-</td>\n",
       "      <td>non-coding gene</td>\n",
       "      <td>GGUCCUCUGACUCUCUUCGGUGACGGGUAUUCUUGGGUGGAUAAUA...</td>\n",
       "      <td>137</td>\n",
       "      <td>hsa-miR-137-5p</td>\n",
       "      <td>ACGGGUAUUCUUGGGUGGAUAAU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>NR_046105.1</td>\n",
       "      <td>MIR137HG</td>\n",
       "      <td>-</td>\n",
       "      <td>61694.0</td>\n",
       "      <td>2469</td>\n",
       "      <td>hsa-mir-137</td>\n",
       "      <td>-</td>\n",
       "      <td>non-coding gene</td>\n",
       "      <td>GGUCCUCUGACUCUCUUCGGUGACGGGUAUUCUUGGGUGGAUAAUA...</td>\n",
       "      <td>137</td>\n",
       "      <td>hsa-miR-137-3p</td>\n",
       "      <td>UUAUUGCUUAAGAAUACGCGUAG</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>329</th>\n",
       "      <td>XM_047441696.1</td>\n",
       "      <td>LOC124905135</td>\n",
       "      <td>+</td>\n",
       "      <td>69285.0</td>\n",
       "      <td>16367</td>\n",
       "      <td>hsa-mir-4763</td>\n",
       "      <td>+</td>\n",
       "      <td>protein-coding gene</td>\n",
       "      <td>CCUGUCCCUCCUGCCCUGCGCCUGCCCAGCCCUCCUGCUCUGGUGA...</td>\n",
       "      <td>4763</td>\n",
       "      <td>hsa-miR-4763-3p</td>\n",
       "      <td>AGGCAGGGGCUGGUGCUGGGCGGG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>330</th>\n",
       "      <td>XM_047441696.1</td>\n",
       "      <td>LOC124905135</td>\n",
       "      <td>+</td>\n",
       "      <td>69285.0</td>\n",
       "      <td>16367</td>\n",
       "      <td>hsa-let-7b</td>\n",
       "      <td>+</td>\n",
       "      <td>protein-coding gene</td>\n",
       "      <td>CGGGGUGAGGUAGUAGGUUGUGUGGUUUCAGGGCAGUGAUGUUGCC...</td>\n",
       "      <td>7b</td>\n",
       "      <td>hsa-let-7b-5p</td>\n",
       "      <td>UGAGGUAGUAGGUUGUGUGGUU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>331</th>\n",
       "      <td>XM_047441696.1</td>\n",
       "      <td>LOC124905135</td>\n",
       "      <td>+</td>\n",
       "      <td>69285.0</td>\n",
       "      <td>16367</td>\n",
       "      <td>hsa-let-7b</td>\n",
       "      <td>+</td>\n",
       "      <td>protein-coding gene</td>\n",
       "      <td>CGGGGUGAGGUAGUAGGUUGUGUGGUUUCAGGGCAGUGAUGUUGCC...</td>\n",
       "      <td>7b</td>\n",
       "      <td>hsa-let-7b-3p</td>\n",
       "      <td>CUAUACAACCUACUGCCUUCCC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>332</th>\n",
       "      <td>XR_002958733.2</td>\n",
       "      <td>LOC112268288</td>\n",
       "      <td>+</td>\n",
       "      <td>11753.0</td>\n",
       "      <td>11634</td>\n",
       "      <td>hsa-mir-3619</td>\n",
       "      <td>+</td>\n",
       "      <td>non-coding gene</td>\n",
       "      <td>ACGGCAUCUUUGCACUCAGCAGGCAGGCUGGUGCAGCCCGUGGUGG...</td>\n",
       "      <td>3619</td>\n",
       "      <td>hsa-miR-3619-5p</td>\n",
       "      <td>UCAGCAGGCAGGCUGGUGCAGC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>333</th>\n",
       "      <td>XR_002958733.2</td>\n",
       "      <td>LOC112268288</td>\n",
       "      <td>+</td>\n",
       "      <td>11753.0</td>\n",
       "      <td>11634</td>\n",
       "      <td>hsa-mir-3619</td>\n",
       "      <td>+</td>\n",
       "      <td>non-coding gene</td>\n",
       "      <td>ACGGCAUCUUUGCACUCAGCAGGCAGGCUGGUGCAGCCCGUGGUGG...</td>\n",
       "      <td>3619</td>\n",
       "      <td>hsa-miR-3619-3p</td>\n",
       "      <td>GGGACCAUCCUGCCUGCUGUGG</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>334 rows × 12 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    hostgene_NCBI_ID hostgene_Name hostgene_strand  pre_mRNA_length  \\\n",
       "0     XM_047427799.1          COP1               -         209014.0   \n",
       "1        NR_132742.1      MIR34AHG               -          34328.0   \n",
       "2        NR_132742.1      MIR34AHG               -          34328.0   \n",
       "3        NR_046105.1      MIR137HG               -          61694.0   \n",
       "4        NR_046105.1      MIR137HG               -          61694.0   \n",
       "..               ...           ...             ...              ...   \n",
       "329   XM_047441696.1  LOC124905135               +          69285.0   \n",
       "330   XM_047441696.1  LOC124905135               +          69285.0   \n",
       "331   XM_047441696.1  LOC124905135               +          69285.0   \n",
       "332   XR_002958733.2  LOC112268288               +          11753.0   \n",
       "333   XR_002958733.2  LOC112268288               +          11753.0   \n",
       "\n",
       "     mature_host_mRNA_Length      miR_name miR_strand            gene_type  \\\n",
       "0                      19460  hsa-mir-1843          -  protein-coding gene   \n",
       "1                       4157   hsa-mir-34a          -      non-coding gene   \n",
       "2                       4157   hsa-mir-34a          -      non-coding gene   \n",
       "3                       2469   hsa-mir-137          -      non-coding gene   \n",
       "4                       2469   hsa-mir-137          -      non-coding gene   \n",
       "..                       ...           ...        ...                  ...   \n",
       "329                    16367  hsa-mir-4763          +  protein-coding gene   \n",
       "330                    16367    hsa-let-7b          +  protein-coding gene   \n",
       "331                    16367    hsa-let-7b          +  protein-coding gene   \n",
       "332                    11634  hsa-mir-3619          +      non-coding gene   \n",
       "333                    11634  hsa-mir-3619          +      non-coding gene   \n",
       "\n",
       "                                   pre-miRNA_sequences standard_id  \\\n",
       "0    GCAGCGAUCCUACAUAAAUAUAUGGAGGUCUCUGUCUGGCUUAGGA...        1843   \n",
       "1    GGCCAGCUGUGAGUGUUUCUUUGGCAGUGUCUUAGCUGGUUGUUGU...         34a   \n",
       "2    GGCCAGCUGUGAGUGUUUCUUUGGCAGUGUCUUAGCUGGUUGUUGU...         34a   \n",
       "3    GGUCCUCUGACUCUCUUCGGUGACGGGUAUUCUUGGGUGGAUAAUA...         137   \n",
       "4    GGUCCUCUGACUCUCUUCGGUGACGGGUAUUCUUGGGUGGAUAAUA...         137   \n",
       "..                                                 ...         ...   \n",
       "329  CCUGUCCCUCCUGCCCUGCGCCUGCCCAGCCCUCCUGCUCUGGUGA...        4763   \n",
       "330  CGGGGUGAGGUAGUAGGUUGUGUGGUUUCAGGGCAGUGAUGUUGCC...          7b   \n",
       "331  CGGGGUGAGGUAGUAGGUUGUGUGGUUUCAGGGCAGUGAUGUUGCC...          7b   \n",
       "332  ACGGCAUCUUUGCACUCAGCAGGCAGGCUGGUGCAGCCCGUGGUGG...        3619   \n",
       "333  ACGGCAUCUUUGCACUCAGCAGGCAGGCUGGUGCAGCCCGUGGUGG...        3619   \n",
       "\n",
       "     miR_mature_name      mature_miR_sequences  \n",
       "0       hsa-miR-1843      UAUGGAGGUCUCUGUCUGGC  \n",
       "1     hsa-miR-34a-5p    UGGCAGUGUCUUAGCUGGUUGU  \n",
       "2     hsa-miR-34a-3p    CAAUCAGCAAGUAUACUGCCCU  \n",
       "3     hsa-miR-137-5p   ACGGGUAUUCUUGGGUGGAUAAU  \n",
       "4     hsa-miR-137-3p   UUAUUGCUUAAGAAUACGCGUAG  \n",
       "..               ...                       ...  \n",
       "329  hsa-miR-4763-3p  AGGCAGGGGCUGGUGCUGGGCGGG  \n",
       "330    hsa-let-7b-5p    UGAGGUAGUAGGUUGUGUGGUU  \n",
       "331    hsa-let-7b-3p    CUAUACAACCUACUGCCUUCCC  \n",
       "332  hsa-miR-3619-5p    UCAGCAGGCAGGCUGGUGCAGC  \n",
       "333  hsa-miR-3619-3p    GGGACCAUCCUGCCUGCUGUGG  \n",
       "\n",
       "[334 rows x 12 columns]"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merged_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "2db635ae-e2c8-4ad7-b410-60189de64d4a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(201, 10)"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "human_exonic_miR_sequence.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8a747fe1-89b7-4b39-aed7-6d027b0b0afa",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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