{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Creation of RNA alignments from databases"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "AP006878.1/1107433-1107263\tGCCGACAGCGAGGGGACAGUCAGUCUCCUCGCA-GGGCUCGGUACAACCGCCUCCGCAAG\n",
      "BA000001.2/1531413-1531580\tGCCGACAGCGAGGGUACAAUA----CCCUCGCAAGGGCUCGGUCAACCCGCCCCCGCAAG\n",
      "AF468962.1/1-168\tGCCGACAGCGAGGGUACAAUA----CCCUCGCAAGGGCUCGGUCAACCCGCCCCCGCAAG\n",
      "AJ248284.1/11131-11298\tGCCGACAGCGAGGGUACAAU-----CCCUCGCAGGGGCUCGGUCUACCCGCCCCCGCAAG\n",
      "\n",
      "AP006878.1/1107433-1107263\tGU-AUCGGGUUCCGUGAGCGGAGCGUGCUCACGCCGAGCCCACAGGGCCGGGAGCAUCCA\n",
      "BA000001.2/1531413-1531580\tGU-UUCGGGGUCGAUGAGCGGGGUGUGCUCACGCCGAGCCUACAGGGCCGG-UGCAUCCG\n",
      "AF468962.1/1-168\tGU-UUCGGGUUCGAUGAGCGGGGUGUGCUCACGCCGAGCCUACAGGGCCGG-UGCAUCCG\n",
      "AJ248284.1/11131-11298\tGUGUUCGGGUUCGAUGAGCGGGGUGUGCUCACGCCGAGCCCACAGGGCCGG-UGCAUCCG\n",
      "\n",
      "AP006878.1/1107433-1107263\tCCCGCGGGAGCAGUGACCGC-GGGCCUCUGUACCCGGCCCACAUUUCGAUGCCC\n",
      "BA000001.2/1531413-1531580\tCCCGCGGGAUUAAUGACCGCUGGGUCUCUGUUGCCGGCCCACAAUAAAGUUUAA\n",
      "AF468962.1/1-168\tCCCGCGGGAUCAAUGACCGCUGGGUCUCUGUUGCCGGCCCACAAAAGUAUUUUA\n",
      "AJ248284.1/11131-11298\tCCCGCGGGAUCAAUGACCGCCGGGUCUCUGUUGCCGGCCUACAGCAAAAAUUUA\n",
      "\n",
      "2D\t.......(((((((...........)))))))..((((((((....(((((.((((.........))))........)))))...........))))))))...(((((((.........(((((((.........)))).))).........)))))))..............\n"
     ]
    }
   ],
   "source": [
    "from pyrna.db import Rfam\n",
    "rfam = Rfam(use_website = True)\n",
    "aligned_rnas, species, consensus2D = rfam.get_entry(rfam_id = 'RF00058', nse_labels = 0)\n",
    "\n",
    "structural_alignment = to_clustalw(consensus2D, aligned_rnas)\n",
    "print structural_alignment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'diagonals': [],\n",
       " 'directly-linked-helices': [],\n",
       " 'helices': [{'coords': [[0.0, 200], [0.0, 140]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'GCGAGGG', 'CCCUCGC'],\n",
       "    ['AJ248284.1/11131-11298', 'GCGAGGG', 'CCCUCGC'],\n",
       "    ['AF468962.1/1-168', 'GCGAGGG', 'CCCUCGC'],\n",
       "    ['AP006878.1/1107433-1107263', 'GCGAGGG', 'UCCUCGC']],\n",
       "   'location': [[8, 14], [26, 32]],\n",
       "   'name': 'H1',\n",
       "   'quantitative_value': 0.0},\n",
       "  {'coords': [[40.0, 200], [40.0, 130]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'GGGCUCGG', 'CCGAGCCU'],\n",
       "    ['AJ248284.1/11131-11298', 'GGGCUCGG', 'CCGAGCCC'],\n",
       "    ['AF468962.1/1-168', 'GGGCUCGG', 'CCGAGCCU'],\n",
       "    ['AP006878.1/1107433-1107263', 'GGGCUCGG', 'CCGAGCCC']],\n",
       "   'location': [[35, 42], [94, 101]],\n",
       "   'name': 'H2',\n",
       "   'quantitative_value': 0.0},\n",
       "  {'coords': [[40.0, 100.0], [40.0, 60.0]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'CCCGC', 'GCGGG'],\n",
       "    ['AJ248284.1/11131-11298', 'CCCGC', 'GCGGG'],\n",
       "    ['AF468962.1/1-168', 'CCCGC', 'GCGGG'],\n",
       "    ['AP006878.1/1107433-1107263', 'ACCGC', 'GCGGA']],\n",
       "   'location': [[47, 51], [78, 82]],\n",
       "   'name': 'H3',\n",
       "   'quantitative_value': 0.0},\n",
       "  {'coords': [[40.0, 30.0], [40.0, 0.0]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'CCCG', 'CGGG'],\n",
       "    ['AJ248284.1/11131-11298', 'CCCG', 'CGGG'],\n",
       "    ['AF468962.1/1-168', 'CCCG', 'CGGG'],\n",
       "    ['AP006878.1/1107433-1107263', 'UCCG', 'CGGG']],\n",
       "   'location': [[53, 56], [66, 69]],\n",
       "   'name': 'H4',\n",
       "   'quantitative_value': 0.0},\n",
       "  {'coords': [[80.0, 200], [80.0, 140]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'GGGCCGG', 'CCGGCCC'],\n",
       "    ['AJ248284.1/11131-11298', 'GGGCCGG', 'CCGGCCU'],\n",
       "    ['AF468962.1/1-168', 'GGGCCGG', 'CCGGCCC'],\n",
       "    ['AP006878.1/1107433-1107263', 'GGGCCGG', 'CCGGCCC']],\n",
       "   'location': [[105, 111], [154, 160]],\n",
       "   'name': 'H5',\n",
       "   'quantitative_value': 0.0},\n",
       "  {'coords': [[80.0, 110.0], [80.0, 90.0]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'CCC', 'GGG'],\n",
       "    ['AJ248284.1/11131-11298', 'CCC', 'GGG'],\n",
       "    ['AF468962.1/1-168', 'CCC', 'GGG'],\n",
       "    ['AP006878.1/1107433-1107263', 'CCC', 'GGG']],\n",
       "   'location': [[121, 123], [142, 144]],\n",
       "   'name': 'H6',\n",
       "   'quantitative_value': 0.0},\n",
       "  {'coords': [[80.0, 60.0], [80.0, 30.0]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'GCGG', 'CCGC'],\n",
       "    ['AJ248284.1/11131-11298', 'GCGG', 'CCGC'],\n",
       "    ['AF468962.1/1-168', 'GCGG', 'CCGC'],\n",
       "    ['AP006878.1/1107433-1107263', 'GCGG', 'CCGC']],\n",
       "   'location': [[124, 127], [137, 140]],\n",
       "   'name': 'H7',\n",
       "   'quantitative_value': 0.0}],\n",
       " 'junctions': [{'coords': [[0.0, 125]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'UACAAUA'],\n",
       "    ['AJ248284.1/11131-11298', 'UACAAU'],\n",
       "    ['AF468962.1/1-168', 'UACAAUA'],\n",
       "    ['AP006878.1/1107433-1107263', 'GACAGUCAGUC']],\n",
       "   'location': [[14, 26]],\n",
       "   'quantitative_value': 1.920286436967152},\n",
       "  {'coords': [[40.0, 115]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'UCAA', 'GUGUGCUCACG'],\n",
       "    ['AJ248284.1/11131-11298', 'UCUA', 'GUGUGCUCACG'],\n",
       "    ['AF468962.1/1-168', 'UCAA', 'GUGUGCUCACG'],\n",
       "    ['AP006878.1/1107433-1107263', 'UACA', 'GCGUGCUCACG']],\n",
       "   'location': [[42, 47], [82, 94]],\n",
       "   'quantitative_value': 0.0},\n",
       "  {'coords': [[40.0, 45.0]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'C', 'GUCGAUGA'],\n",
       "    ['AJ248284.1/11131-11298', 'C', 'UUCGAUGA'],\n",
       "    ['AF468962.1/1-168', 'C', 'UUCGAUGA'],\n",
       "    ['AP006878.1/1107433-1107263', 'C', 'UUCCGUGA']],\n",
       "   'location': [[51, 53], [69, 78]],\n",
       "   'quantitative_value': 0.0},\n",
       "  {'coords': [[40.0, -15.0]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'CAAGGUUU'],\n",
       "    ['AJ248284.1/11131-11298', 'CAAGGUGUU'],\n",
       "    ['AF468962.1/1-168', 'CAAGGUUU'],\n",
       "    ['AP006878.1/1107433-1107263', 'CAAGGUAU']],\n",
       "   'location': [[56, 66]],\n",
       "   'quantitative_value': 0.4330127018922193},\n",
       "  {'coords': [[80.0, 125]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'UGCAUCCG', 'UCUCUGUUG'],\n",
       "    ['AJ248284.1/11131-11298', 'UGCAUCCG', 'UCUCUGUUG'],\n",
       "    ['AF468962.1/1-168', 'UGCAUCCG', 'UCUCUGUUG'],\n",
       "    ['AP006878.1/1107433-1107263', 'GAGCAUCCA', 'CCUCUGUAC']],\n",
       "   'location': [[111, 121], [144, 154]],\n",
       "   'quantitative_value': 0.4330127018922193},\n",
       "  {'coords': [[80.0, 15.0]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'GAUUAAUGA'],\n",
       "    ['AJ248284.1/11131-11298', 'GAUCAAUGA'],\n",
       "    ['AF468962.1/1-168', 'GAUCAAUGA'],\n",
       "    ['AP006878.1/1107433-1107263', 'GAGCAGUGA']],\n",
       "   'location': [[127, 137]],\n",
       "   'quantitative_value': 0.0},\n",
       "  {'coords': [[80.0, 75.0]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', '', 'U'],\n",
       "    ['AJ248284.1/11131-11298', '', 'C'],\n",
       "    ['AF468962.1/1-168', '', 'U'],\n",
       "    ['AP006878.1/1107433-1107263', '', '']],\n",
       "   'location': [[123, 124], [140, 142]],\n",
       "   'quantitative_value': 0.4330127018922193}],\n",
       " 'single_strands': [{'coords': [[-40.0, 200], [0.0, 200]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'GCCGACA'],\n",
       "    ['AJ248284.1/11131-11298', 'GCCGACA'],\n",
       "    ['AF468962.1/1-168', 'GCCGACA'],\n",
       "    ['AP006878.1/1107433-1107263', 'GCCGACA']],\n",
       "   'location': [1, 7],\n",
       "   'name': 'SS1',\n",
       "   'quantitative_value': 0.0},\n",
       "  {'descriptions': [['BA000001.2/1531413-1531580', 'UACAAUA'],\n",
       "    ['AJ248284.1/11131-11298', 'UACAAU'],\n",
       "    ['AF468962.1/1-168', 'UACAAUA'],\n",
       "    ['AP006878.1/1107433-1107263', 'GACAGUCAGUC']],\n",
       "   'location': [15, 25],\n",
       "   'name': 'SS2',\n",
       "   'quantitative_value': 1.920286436967152},\n",
       "  {'coords': [[0.0, 200], [40.0, 200]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'AA'],\n",
       "    ['AJ248284.1/11131-11298', 'AG'],\n",
       "    ['AF468962.1/1-168', 'AA'],\n",
       "    ['AP006878.1/1107433-1107263', 'A']],\n",
       "   'location': [33, 34],\n",
       "   'name': 'SS3',\n",
       "   'quantitative_value': 0.4330127018922193},\n",
       "  {'descriptions': [['BA000001.2/1531413-1531580', 'UCAA'],\n",
       "    ['AJ248284.1/11131-11298', 'UCUA'],\n",
       "    ['AF468962.1/1-168', 'UCAA'],\n",
       "    ['AP006878.1/1107433-1107263', 'UACA']],\n",
       "   'location': [43, 46],\n",
       "   'name': 'SS4',\n",
       "   'quantitative_value': 0.0},\n",
       "  {'descriptions': [['BA000001.2/1531413-1531580', 'C'],\n",
       "    ['AJ248284.1/11131-11298', 'C'],\n",
       "    ['AF468962.1/1-168', 'C'],\n",
       "    ['AP006878.1/1107433-1107263', 'C']],\n",
       "   'location': [52, 52],\n",
       "   'name': 'SS5',\n",
       "   'quantitative_value': 0.0},\n",
       "  {'descriptions': [['BA000001.2/1531413-1531580', 'CAAGGUUU'],\n",
       "    ['AJ248284.1/11131-11298', 'CAAGGUGUU'],\n",
       "    ['AF468962.1/1-168', 'CAAGGUUU'],\n",
       "    ['AP006878.1/1107433-1107263', 'CAAGGUAU']],\n",
       "   'location': [57, 65],\n",
       "   'name': 'SS6',\n",
       "   'quantitative_value': 0.4330127018922193},\n",
       "  {'descriptions': [['BA000001.2/1531413-1531580', 'GUCGAUGA'],\n",
       "    ['AJ248284.1/11131-11298', 'UUCGAUGA'],\n",
       "    ['AF468962.1/1-168', 'UUCGAUGA'],\n",
       "    ['AP006878.1/1107433-1107263', 'UUCCGUGA']],\n",
       "   'location': [70, 77],\n",
       "   'name': 'SS7',\n",
       "   'quantitative_value': 0.0},\n",
       "  {'descriptions': [['BA000001.2/1531413-1531580', 'GUGUGCUCACG'],\n",
       "    ['AJ248284.1/11131-11298', 'GUGUGCUCACG'],\n",
       "    ['AF468962.1/1-168', 'GUGUGCUCACG'],\n",
       "    ['AP006878.1/1107433-1107263', 'GCGUGCUCACG']],\n",
       "   'location': [83, 93],\n",
       "   'name': 'SS8',\n",
       "   'quantitative_value': 0.0},\n",
       "  {'coords': [[40.0, 200], [80.0, 200]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'ACA'],\n",
       "    ['AJ248284.1/11131-11298', 'ACA'],\n",
       "    ['AF468962.1/1-168', 'ACA'],\n",
       "    ['AP006878.1/1107433-1107263', 'ACA']],\n",
       "   'location': [102, 104],\n",
       "   'name': 'SS9',\n",
       "   'quantitative_value': 0.0},\n",
       "  {'descriptions': [['BA000001.2/1531413-1531580', 'UGCAUCCG'],\n",
       "    ['AJ248284.1/11131-11298', 'UGCAUCCG'],\n",
       "    ['AF468962.1/1-168', 'UGCAUCCG'],\n",
       "    ['AP006878.1/1107433-1107263', 'GAGCAUCCA']],\n",
       "   'location': [112, 120],\n",
       "   'name': 'SS10',\n",
       "   'quantitative_value': 0.4330127018922193},\n",
       "  {'descriptions': [['BA000001.2/1531413-1531580', 'GAUUAAUGA'],\n",
       "    ['AJ248284.1/11131-11298', 'GAUCAAUGA'],\n",
       "    ['AF468962.1/1-168', 'GAUCAAUGA'],\n",
       "    ['AP006878.1/1107433-1107263', 'GAGCAGUGA']],\n",
       "   'location': [128, 136],\n",
       "   'name': 'SS11',\n",
       "   'quantitative_value': 0.0},\n",
       "  {'descriptions': [['BA000001.2/1531413-1531580', 'U'],\n",
       "    ['AJ248284.1/11131-11298', 'C'],\n",
       "    ['AF468962.1/1-168', 'U'],\n",
       "    ['AP006878.1/1107433-1107263', '']],\n",
       "   'location': [141, 141],\n",
       "   'name': 'SS12',\n",
       "   'quantitative_value': 0.4330127018922193},\n",
       "  {'descriptions': [['BA000001.2/1531413-1531580', 'UCUCUGUUG'],\n",
       "    ['AJ248284.1/11131-11298', 'UCUCUGUUG'],\n",
       "    ['AF468962.1/1-168', 'UCUCUGUUG'],\n",
       "    ['AP006878.1/1107433-1107263', 'CCUCUGUAC']],\n",
       "   'location': [145, 153],\n",
       "   'name': 'SS13',\n",
       "   'quantitative_value': 0.0},\n",
       "  {'coords': [[80.0, 200], [120.0, 200]],\n",
       "   'descriptions': [['BA000001.2/1531413-1531580', 'ACAAUAAAGUUUAA'],\n",
       "    ['AJ248284.1/11131-11298', 'ACAGCAAAAAUUUA'],\n",
       "    ['AF468962.1/1-168', 'ACAAAAGUAUUUUA'],\n",
       "    ['AP006878.1/1107433-1107263', 'ACAUUUCGAUGCCC']],\n",
       "   'location': [161, 174],\n",
       "   'name': 'SS14',\n",
       "   'quantitative_value': 0.0}]}"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "consensus2d_to_booquet(structural_alignment)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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