genbank-scraping.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# GenBanK -> Web Scraping"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Duarte Velho PG53481\n",
    "Introdução aos algoritemos e à programação\n",
    "Janeiro de 2024\n",
    "\n",
    "## Web Scraping\n",
    "De um modo simples, web scraping refere-se à utilização de programas para ir buscar conteúdos de um determinado site e extrair de lá a informação que nos interessa, com o intuito de sistematizar a recolha de dados a partir do site (Neste caso,o Genbank)\n",
    "\n",
    "O GenBank é um site que contém informação de milhares de sequências. Em vez de irmos buscar uma a uma, podemos escrever um programa que vai buscar sequência a sequência, e para cada, extrair a informação que nos interessa, de forma automática. Fazer a mesma coisa manualmente seria uma tarefa muito morosa e estaria sujeita a erros humanos. (Fonte retirada do enunciado do Docente Jorge Rocha [Repositório](https://github.com/jgrocha/m8-ferramentas))\n",
    "\n",
    "Protocolo HTTP - protocolo usado para a comunicação entre os servidores e os navegadores.\n",
    "\n",
    "#### Como funciona o carregamento de uma página\n",
    "\n",
    "Quando se pede uma página, o navegador faz um pedido inicial ao respetivo servidor e interpreta essa resposta. A resposta é tipicamente um documento HTML que faz referências a imagens, scripts, estilos, etc, que também têm que ser descarregados pelo navegador para poder renderizar a página pedida. Ou seja, um pedido inicial de uma página, na prática pode dar origem a dezenas de novos pedidos. Só com toda essa informação é que a página pode ser devidamente apresentada ao utilizador.\n",
    "Para além dos conteúdos iniciais, mesmo depois da página ser carregada e renderizada, podem ser despoletados novos pedidos ao servidor assincronamente a partir de scripts na página. Estes são designados pedidos AJAX. (Fonte retirada do enunciado do Docente Jorge Rocha [Repositório](https://github.com/jgrocha/m8-ferramentas))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [],
   "source": [
    "#packages usadas\n",
    "#pip install pymysql"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Bibliotecas\n",
    "import requests\n",
    "from bs4 import BeautifulSoup\n",
    "import re \n",
    "import pandas as pd\n",
    "import time\n",
    "import pymysql"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [],
   "source": [
    "URL = 'https://www.ncbi.nlm.nih.gov/nuccore/NM_003742' #Gene ABCB11"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get da página que contrém o registo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [],
   "source": [
    "r = requests.get(URL)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Parsing the HTML"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[<meta content=\"text/html; charset=utf-8\" http-equiv=\"Content-Type\"/>,\n",
       " <meta content=\"index,nofollow,noarchive\" name=\"robots\"/>,\n",
       " <meta content=\"entrez\" name=\"ncbi_app\"/>,\n",
       " <meta content=\"nuccore\" name=\"ncbi_db\"/>,\n",
       " <meta content=\"genbank\" name=\"ncbi_report\"/>,\n",
       " <meta content=\"html\" name=\"ncbi_format\"/>,\n",
       " <meta content=\"20\" name=\"ncbi_pagesize\"/>,\n",
       " <meta content=\"default\" name=\"ncbi_sortorder\"/>,\n",
       " <meta content=\"1\" name=\"ncbi_pageno\"/>,\n",
       " <meta content=\"1\" name=\"ncbi_resultcount\"/>,\n",
       " <meta content=\"retrieve\" name=\"ncbi_op\"/>,\n",
       " <meta content=\"genbank\" name=\"ncbi_pdid\"/>,\n",
       " <meta content=\"CE89A24E5A5C2A61_1571SID\" name=\"ncbi_sessionid\"/>,\n",
       " <meta content=\"1387699148\" name=\"ncbi_uidlist\"/>,\n",
       " <meta content=\"all\" name=\"ncbi_filter\"/>,\n",
       " <meta content=\"false\" name=\"ncbi_stat\"/>,\n",
       " <meta content=\"true\" name=\"ncbi_hitstat\"/>,\n",
       " <meta content=\"CE89A24E5A596B11000000000623055D.m_32\" name=\"ncbi_phid\"/>,\n",
       " <meta content=\"origin-when-cross-origin\" name=\"referrer\"/>]"
      ]
     },
     "execution_count": 44,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "soup = BeautifulSoup(r.content, 'html.parser')\n",
    "soup.find_all('meta')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Get do id do gene ABCB11 na base de dados"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [],
   "source": [
    "id = soup.find_all('meta',{'name':'ncbi_uidlist'})[0].attrs['content']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "LOCUS       NM_003742               6934 bp    mRNA    linear   PRI 21-NOV-2023\n",
      "DEFINITION  Homo sapiens ATP binding cassette subfamily B member 11 (ABCB11),\n",
      "            mRNA.\n",
      "ACCESSION   NM_003742\n",
      "VERSION     NM_003742.4\n",
      "KEYWORDS    RefSeq; MANE Select.\n",
      "SOURCE      Homo sapiens (human)\n",
      "  ORGANISM  Homo sapiens\n",
      "            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;\n",
      "            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;\n",
      "            Catarrhini; Hominidae; Homo.\n",
      "REFERENCE   1  (bases 1 to 6934)\n",
      "  AUTHORS   Liu H, Irobalieva RN, Kowal J, Ni D, Nosol K, Bang-Sorensen R,\n",
      "            Lancien L, Stahlberg H, Stieger B and Locher KP.\n",
      "  TITLE     Structural basis of bile salt extrusion and small-molecule\n",
      "            inhibition in human BSEP\n",
      "  JOURNAL   Nat Commun 14 (1), 7296 (2023)\n",
      "   PUBMED   37949847\n",
      "  REMARK    GeneRIF: Structural basis of bile salt extrusion and small-molecule\n",
      "            inhibition in human BSEP.\n",
      "            Publication Status: Online-Only\n",
      "REFERENCE   2  (bases 1 to 6934)\n",
      "  AUTHORS   Pfister ED, Jaeger VK, Karch A, Shay D, Schukfeh N, Ohlendorf J,\n",
      "            Junge N, Goldschmidt I, Stalke A, Keitel-Anselmino V and Baumann U.\n",
      "  TITLE     Native liver survival in bile salt export pump deficiency: results\n",
      "            of a retrospective cohort study\n",
      "  JOURNAL   Hepatol Commun 7 (4), e0092 (2023)\n",
      "   PUBMED   36995996\n",
      "  REMARK    GeneRIF: Native liver survival in bile salt export pump deficiency:\n",
      "            results of a retrospective cohort study.\n",
      "            Publication Status: Online-Only\n",
      "REFERENCE   3  (bases 1 to 6934)\n",
      "  AUTHORS   Nayagam JS, Foskett P, Strautnieks S, Agarwal K, Miquel R, Joshi D\n",
      "            and Thompson RJ.\n",
      "  TITLE     Clinical phenotype of adult-onset liver disease in patients with\n",
      "            variants in ABCB4, ABCB11, and ATP8B1\n",
      "  JOURNAL   Hepatol Commun 6 (10), 2654-2664 (2022)\n",
      "   PUBMED   35894240\n",
      "  REMARK    GeneRIF: Clinical phenotype of adult-onset liver disease in\n",
      "            patients with variants in ABCB4, ABCB11, and ATP8B1.\n",
      "REFERENCE   4  (bases 1 to 6934)\n",
      "  AUTHORS   Selim N, Omair H, El-Karaksy H, Fathy M, Mahmoud E, Baroudy S,\n",
      "            Fathy M and Yassin N.\n",
      "  TITLE     A study of exons 14, 15, and 24 of the ABCB11 gene in Egyptian\n",
      "            children with normal GGT cholestasis\n",
      "  JOURNAL   Arab J Gastroenterol 23 (1), 15-19 (2022)\n",
      "   PUBMED   35153175\n",
      "  REMARK    GeneRIF: A study of exons 14, 15, and 24 of the ABCB11 gene in\n",
      "            Egyptian children with normal GGT cholestasis.\n",
      "REFERENCE   5  (bases 1 to 6934)\n",
      "  AUTHORS   Wang R, Salem M, Yousef IM, Tuchweber B, Lam P, Childs SJ, Helgason\n",
      "            CD, Ackerley C, Phillips MJ and Ling V.\n",
      "  TITLE     Targeted inactivation of sister of P-glycoprotein gene (spgp) in\n",
      "            mice results in nonprogressive but persistent intrahepatic\n",
      "            cholestasis\n",
      "  JOURNAL   Proc Natl Acad Sci U S A 98 (4), 2011-2016 (2001)\n",
      "   PUBMED   11172067\n",
      "REFERENCE   6  (bases 1 to 6934)\n",
      "  AUTHORS   Jansen PL, Strautnieks SS, Jacquemin E, Hadchouel M, Sokal EM,\n",
      "            Hooiveld GJ, Koning JH, De Jager-Krikken A, Kuipers F, Stellaard F,\n",
      "            Bijleveld CM, Gouw A, Van Goor H, Thompson RJ and Muller M.\n",
      "  TITLE     Hepatocanalicular bile salt export pump deficiency in patients with\n",
      "            progressive familial intrahepatic cholestasis\n",
      "  JOURNAL   Gastroenterology 117 (6), 1370-1379 (1999)\n",
      "   PUBMED   10579978\n",
      "REFERENCE   7  (bases 1 to 6934)\n",
      "  AUTHORS   Strautnieks SS, Bull LN, Knisely AS, Kocoshis SA, Dahl N, Arnell H,\n",
      "            Sokal E, Dahan K, Childs S, Ling V, Tanner MS, Kagalwalla AF,\n",
      "            Nemeth A, Pawlowska J, Baker A, Mieli-Vergani G, Freimer NB,\n",
      "            Gardiner RM and Thompson RJ.\n",
      "  TITLE     A gene encoding a liver-specific ABC transporter is mutated in\n",
      "            progressive familial intrahepatic cholestasis\n",
      "  JOURNAL   Nat Genet 20 (3), 233-238 (1998)\n",
      "   PUBMED   9806540\n",
      "REFERENCE   8  (bases 1 to 6934)\n",
      "  AUTHORS   Gerloff T, Stieger B, Hagenbuch B, Madon J, Landmann L, Roth J,\n",
      "            Hofmann AF and Meier PJ.\n",
      "  TITLE     The sister of P-glycoprotein represents the canalicular bile salt\n",
      "            export pump of mammalian liver\n",
      "  JOURNAL   J Biol Chem 273 (16), 10046-10050 (1998)\n",
      "   PUBMED   9545351\n",
      "REFERENCE   9  (bases 1 to 6934)\n",
      "  AUTHORS   Amendola,M. and Squires,J.E.\n",
      "  TITLE     Pediatric Genetic Cholestatic Liver Disease Overview\n",
      "  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH,\n",
      "            Gripp KW and Amemiya A (Eds.);\n",
      "            GENEREVIEWS(R);\n",
      "            (1993)\n",
      "   PUBMED   36108118\n",
      "REFERENCE   10 (bases 1 to 6934)\n",
      "  AUTHORS   Bull,L.N., Morotti,R. and Squires,J.E.\n",
      "  TITLE     ATP8B1 Deficiency\n",
      "  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH,\n",
      "            Gripp KW and Amemiya A (Eds.);\n",
      "            GENEREVIEWS(R);\n",
      "            (1993)\n",
      "   PUBMED   20301474\n",
      "COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The\n",
      "            reference sequence was derived from AC008177.3, AF091582.1,\n",
      "            AC069137.6 and CB161524.1.\n",
      "            This sequence is a reference standard in the RefSeqGene project.\n",
      "            \n",
      "            On May 8, 2018 this sequence version replaced NM_003742.3.\n",
      "            \n",
      "            Summary: The membrane-associated protein encoded by this gene is a\n",
      "            member of the superfamily of ATP-binding cassette (ABC)\n",
      "            transporters. ABC proteins transport various molecules across\n",
      "            extra- and intra-cellular membranes. ABC genes are divided into\n",
      "            seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20,\n",
      "            White). This protein is a member of the MDR/TAP subfamily. Members\n",
      "            of the MDR/TAP subfamily are involved in multidrug resistance. The\n",
      "            protein encoded by this gene is the major canalicular bile salt\n",
      "            export pump in man. Mutations in this gene cause a form of\n",
      "            progressive familial intrahepatic cholestases which are a group of\n",
      "            inherited disorders with severe cholestatic liver disease from\n",
      "            early infancy. [provided by RefSeq, Jul 2008].\n",
      "            \n",
      "            Sequence Note: This RefSeq record was created from transcript and\n",
      "            genomic sequence data to make the sequence consistent with the\n",
      "            reference genome assembly. The genomic coordinates used for the\n",
      "            transcript record were based on transcript alignments.\n",
      "            \n",
      "            Publication Note:  This RefSeq record includes a subset of the\n",
      "            publications that are available for this gene. Please see the Gene\n",
      "            record to access additional publications.\n",
      "            \n",
      "            ##Evidence-Data-START##\n",
      "            Transcript exon combination :: AF091582.1, AF136523.1 [ECO:0000332]\n",
      "            RNAseq introns              :: mixed sample support SAMEA1965299,\n",
      "                                           SAMEA1966682 [ECO:0006172]\n",
      "            ##Evidence-Data-END##\n",
      "            \n",
      "            ##RefSeq-Attributes-START##\n",
      "            MANE Ensembl match     :: ENST00000650372.1/ ENSP00000497931.1\n",
      "            RefSeq Select criteria :: based on manual assertion, conservation,\n",
      "                                      expression\n",
      "            ##RefSeq-Attributes-END##\n",
      "            COMPLETENESS: complete on the 3' end.\n",
      "PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP\n",
      "            1-1                 AC008177.3         92136-92136         c\n",
      "            2-1141              AF091582.1         1-1140\n",
      "            1142-1142           AC008177.3         46990-46990         c\n",
      "            1143-4169           AF091582.1         1142-4168\n",
      "            4170-6928           AC069137.6         90425-93183         c\n",
      "            6929-6934           CB161524.1         17-22               c\n",
      "FEATURES             Location/Qualifiers\n",
      "     source          1..6934\n",
      "                     /organism=\"Homo sapiens\"\n",
      "                     /mol_type=\"mRNA\"\n",
      "                     /db_xref=\"taxon:9606\"\n",
      "                     /chromosome=\"2\"\n",
      "                     /map=\"2q31.1\"\n",
      "     gene            1..6934\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"ATP binding cassette subfamily B member 11\"\n",
      "                     /db_xref=\"GeneID:8647\"\n",
      "                     /db_xref=\"HGNC:HGNC:42\"\n",
      "                     /db_xref=\"MIM:603201\"\n",
      "     exon            1..100\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     misc_feature    8..10\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"upstream in-frame stop codon\"\n",
      "     exon            101..203\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     CDS             128..4093\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"progressive familial intrahepatic cholestasis 2;\n",
      "                     ABC member 16, MDR/TAP subfamily; sister p-glycoprotein;\n",
      "                     ATP-binding cassette sub-family B member 11; ATP-binding\n",
      "                     cassette, sub-family B (MDR/TAP), member 11\"\n",
      "                     /codon_start=1\n",
      "                     /product=\"bile salt export pump\"\n",
      "                     /protein_id=\"NP_003733.2\"\n",
      "                     /db_xref=\"CCDS:CCDS46444.1\"\n",
      "                     /db_xref=\"GeneID:8647\"\n",
      "                     /db_xref=\"HGNC:HGNC:42\"\n",
      "                     /db_xref=\"MIM:603201\"\n",
      "                     /translation=\"MSDSVILRSIKKFGEENDGFESDKSYNNDKKSRLQDEKKGDGVR\n",
      "                     VGFFQLFRFSSSTDIWLMFVGSLCAFLHGIAQPGVLLIFGTMTDVFIDYDVELQELQI\n",
      "                     PGKACVNNTIVWTNSSLNQNMTNGTRCGLLNIESEMIKFASYYAGIAVAVLITGYIQI\n",
      "                     CFWVIAAARQIQKMRKFYFRRIMRMEIGWFDCNSVGELNTRFSDDINKINDAIADQMA\n",
      "                     LFIQRMTSTICGFLLGFFRGWKLTLVIISVSPLIGIGAATIGLSVSKFTDYELKAYAK\n",
      "                     AGVVADEVISSMRTVAAFGGEKREVERYEKNLVFAQRWGIRKGIVMGFFTGFVWCLIF\n",
      "                     LCYALAFWYGSTLVLDEGEYTPGTLVQIFLSVIVGALNLGNASPCLEAFATGRAAATS\n",
      "                     IFETIDRKPIIDCMSEDGYKLDRIKGEIEFHNVTFHYPSRPEVKILNDLNMVIKPGEM\n",
      "                     TALVGPSGAGKSTALQLIQRFYDPCEGMVTVDGHDIRSLNIQWLRDQIGIVEQEPVLF\n",
      "                     STTIAENIRYGREDATMEDIVQAAKEANAYNFIMDLPQQFDTLVGEGGGQMSGGQKQR\n",
      "                     VAIARALIRNPKILLLDMATSALDNESEAMVQEVLSKIQHGHTIISVAHRLSTVRAAD\n",
      "                     TIIGFEHGTAVERGTHEELLERKGVYFTLVTLQSQGNQALNEEDIKDATEDDMLARTF\n",
      "                     SRGSYQDSLRASIRQRSKSQLSYLVHEPPLAVVDHKSTYEEDRKDKDIPVQEEVEPAP\n",
      "                     VRRILKFSAPEWPYMLVGSVGAAVNGTVTPLYAFLFSQILGTFSIPDKEEQRSQINGV\n",
      "                     CLLFVAMGCVSLFTQFLQGYAFAKSGELLTKRLRKFGFRAMLGQDIAWFDDLRNSPGA\n",
      "                     LTTRLATDASQVQGAAGSQIGMIVNSFTNVTVAMIIAFSFSWKLSLVILCFFPFLALS\n",
      "                     GATQTRMLTGFASRDKQALEMVGQITNEALSNIRTVAGIGKERRFIEALETELEKPFK\n",
      "                     TAIQKANIYGFCFAFAQCIMFIANSASYRYGGYLISNEGLHFSYVFRVISAVVLSATA\n",
      "                     LGRAFSYTPSYAKAKISAARFFQLLDRQPPISVYNTAGEKWDNFQGKIDFVDCKFTYP\n",
      "                     SRPDSQVLNGLSVSISPGQTLAFVGSSGCGKSTSIQLLERFYDPDQGKVMIDGHDSKK\n",
      "                     VNVQFLRSNIGIVSQEPVLFACSIMDNIKYGDNTKEIPMERVIAAAKQAQLHDFVMSL\n",
      "                     PEKYETNVGSQGSQLSRGEKQRIAIARAIVRDPKILLLDEATSALDTESEKTVQVALD\n",
      "                     KAREGRTCIVIAHRLSTIQNADIIAVMAQGVVIEKGTHEELMAQKGAYYKLVTTGSPI\n",
      "                     S\"\n",
      "     misc_feature    173..238\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite\"\n",
      "     misc_feature    314..376\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     transmembrane region\"\n",
      "     misc_feature    452..454\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"N-linked (GlcNAc...) asparagine.\n",
      "                     /evidence=ECO:0000269|PubMed:17082223; propagated from\n",
      "                     UniProtKB/Swiss-Prot (O95342.2); glycosylation site\"\n",
      "     misc_feature    473..475\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"N-linked (GlcNAc...) asparagine.\n",
      "                     /evidence=ECO:0000269|PubMed:17082223; propagated from\n",
      "                     UniProtKB/Swiss-Prot (O95342.2); glycosylation site\"\n",
      "     misc_feature    491..493\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"N-linked (GlcNAc...) asparagine.\n",
      "                     /evidence=ECO:0000269|PubMed:17082223; propagated from\n",
      "                     UniProtKB/Swiss-Prot (O95342.2); glycosylation site\"\n",
      "     misc_feature    500..502\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"N-linked (GlcNAc...) asparagine.\n",
      "                     /evidence=ECO:0000269|PubMed:17082223; propagated from\n",
      "                     UniProtKB/Swiss-Prot (O95342.2); glycosylation site\"\n",
      "     misc_feature    569..631\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     transmembrane region\"\n",
      "     misc_feature    773..835\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     transmembrane region\"\n",
      "     misc_feature    848..910\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     transmembrane region\"\n",
      "     misc_feature    1085..1147\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     transmembrane region\"\n",
      "     misc_feature    1187..1249\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     transmembrane region\"\n",
      "     misc_feature    1883..1885\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"Phosphothreonine.\n",
      "                     /evidence=ECO:0007744|PubMed:24275569; propagated from\n",
      "                     UniProtKB/Swiss-Prot (O95342.2); phosphorylation site\"\n",
      "     misc_feature    1886..1888\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"Phosphoserine.\n",
      "                     /evidence=ECO:0007744|PubMed:24275569; propagated from\n",
      "                     UniProtKB/Swiss-Prot (O95342.2); phosphorylation site\"\n",
      "     misc_feature    2078..2143\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     Region: Interaction with HAX1. /evidence=ECO:0000250\"\n",
      "     misc_feature    2195..2197\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"Phosphoserine.\n",
      "                     /evidence=ECO:0000250|UniProtKB:Q9QY30; propagated from\n",
      "                     UniProtKB/Swiss-Prot (O95342.2); phosphorylation site\"\n",
      "     misc_feature    2228..2230\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"Phosphoserine.\n",
      "                     /evidence=ECO:0000250|UniProtKB:O70127; propagated from\n",
      "                     UniProtKB/Swiss-Prot (O95342.2); phosphorylation site\"\n",
      "     misc_feature    2237..2239\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"Phosphoserine.\n",
      "                     /evidence=ECO:0007744|PubMed:24275569; propagated from\n",
      "                     UniProtKB/Swiss-Prot (O95342.2); phosphorylation site\"\n",
      "     misc_feature    2393..2455\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     transmembrane region\"\n",
      "     misc_feature    2510..2572\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     transmembrane region\"\n",
      "     misc_feature    2735..2797\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     transmembrane region\"\n",
      "     misc_feature    2798..2860\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     transmembrane region\"\n",
      "     misc_feature    3065..3127\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     transmembrane region\"\n",
      "     misc_feature    3161..3223\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     transmembrane region\"\n",
      "     misc_feature    3767..3769\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"Phosphoserine.\n",
      "                     /evidence=ECO:0007744|PubMed:24275569; propagated from\n",
      "                     UniProtKB/Swiss-Prot (O95342.2); phosphorylation site\"\n",
      "     misc_feature    4058..4069\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"propagated from UniProtKB/Swiss-Prot (O95342.2);\n",
      "                     Region: Mediates internalization from the plasma membrane.\n",
      "                     /evidence=ECO:0000269|PubMed:22262466\"\n",
      "     misc_feature    4088..4090\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"Phosphoserine.\n",
      "                     /evidence=ECO:0000250|UniProtKB:O70127; propagated from\n",
      "                     UniProtKB/Swiss-Prot (O95342.2); phosphorylation site\"\n",
      "     exon            204..225\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            226..277\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            278..516\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            517..604\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            605..738\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            739..910\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            911..1035\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            1036..1210\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            1211..1324\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            1325..1435\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            1436..1561\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            1562..1765\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            1766..1936\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            1937..2138\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            2139..2202\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            2203..2305\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            2306..2470\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            2471..2575\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            2576..2737\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            2738..2941\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            2942..3183\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            3184..3340\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            3341..3538\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            3539..3745\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            3746..3892\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     exon            3893..6934\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /inference=\"alignment:Splign:2.1.0\"\n",
      "     regulatory      6207..6212\n",
      "                     /regulatory_class=\"polyA_signal_sequence\"\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "                     /note=\"hexamer: AATAAA\"\n",
      "     polyA_site      6229\n",
      "                     /gene=\"ABCB11\"\n",
      "                     /gene_synonym=\"ABC16; BRIC2; BSEP; PFIC-2; PFIC2; PGY4;\n",
      "                     SPGP\"\n",
      "ORIGIN      \n",
      "        1 agaatgatga aaaccgaggt tggaaaaggt tgtgaaacct tttaactctc cacagtggag\n",
      "       61 tccattattt cctctggctt cctcaaattc atattcacag ggtcgttggc tgtgggttgc\n",
      "      121 aattaccatg tctgactcag taattcttcg aagtataaag aaatttggag aggagaatga\n",
      "      181 tggttttgag tcagataaat catataataa tgataagaaa tcaaggttac aagatgagaa\n",
      "      241 gaaaggtgat ggcgttagag ttggcttctt tcaattgttt cggttttctt catcaactga\n",
      "      301 catttggctg atgtttgtgg gaagtttgtg tgcatttctc catggaatag cccagccagg\n",
      "      361 cgtgctactc atttttggca caatgacaga tgtttttatt gactacgacg ttgagttaca\n",
      "      421 agaactccag attccaggaa aagcatgtgt gaataacacc attgtatgga ctaacagttc\n",
      "      481 cctcaaccag aacatgacaa atggaacacg ttgtgggttg ctgaacatcg agagcgaaat\n",
      "      541 gatcaaattt gccagttact atgctggaat tgctgtcgca gtacttatca caggatatat\n",
      "      601 tcaaatatgc ttttgggtca ttgccgcagc tcgtcagata cagaaaatga gaaaatttta\n",
      "      661 ctttaggaga ataatgagaa tggaaatagg gtggtttgac tgcaattcag tgggggagct\n",
      "      721 gaatacaaga ttctctgatg atattaataa aatcaatgat gccatagctg accaaatggc\n",
      "      781 ccttttcatt cagcgcatga cctcgaccat ctgtggtttc ctgttgggat ttttcagggg\n",
      "      841 ttggaaactg accttggtta ttatttctgt cagccctctc attgggattg gagcagccac\n",
      "      901 cattggtctg agtgtgtcca agtttacgga ctatgagctg aaggcctatg ccaaagcagg\n",
      "      961 ggtggtggct gatgaagtca tttcatcaat gagaacagtg gctgcttttg gtggtgagaa\n",
      "     1021 aagagaggtt gaaaggtatg agaaaaatct tgtgttcgcc cagcgttggg gaattagaaa\n",
      "     1081 aggaatagtg atgggattct ttactggatt cgtgtggtgt ctcatctttt tgtgttatgc\n",
      "     1141 actggccttc tggtacggct ccacacttgt cctggatgaa ggagaatata caccaggaac\n",
      "     1201 ccttgtccag attttcctca gtgtcatagt aggagcttta aatcttggca atgcctctcc\n",
      "     1261 ttgtttggaa gcctttgcaa ctggacgtgc agcagccacc agcatttttg agacaataga\n",
      "     1321 caggaaaccc atcattgact gcatgtcaga agatggttac aagttggatc gaatcaaggg\n",
      "     1381 tgaaattgaa ttccataatg tgaccttcca ttatccttcc agaccagagg tgaagattct\n",
      "     1441 aaatgacctc aacatggtca ttaaaccagg ggaaatgaca gctctggtag gacccagtgg\n",
      "     1501 agctggaaaa agtacagcac tgcaactcat tcagcgattc tatgacccct gtgaaggaat\n",
      "     1561 ggtgaccgtg gatggccatg acattcgctc tcttaacatt cagtggctta gagatcagat\n",
      "     1621 tgggatagtg gagcaagagc cagttctgtt ctctaccacc attgcagaaa atattcgcta\n",
      "     1681 tggcagagaa gatgcaacaa tggaagacat agtccaagct gccaaggagg ccaatgccta\n",
      "     1741 caacttcatc atggacctgc cacagcaatt tgacaccctt gttggagaag gaggaggcca\n",
      "     1801 gatgagtggt ggccagaaac aaagggtagc tatcgccaga gccctcatcc gaaatcccaa\n",
      "     1861 gattctgctt ttggacatgg ccacctcagc tctggacaat gagagtgaag ccatggtgca\n",
      "     1921 agaagtgctg agtaagattc agcatgggca cacaatcatt tcagttgctc atcgcttgtc\n",
      "     1981 tacggtcaga gctgcagata ccatcattgg ttttgaacat ggcactgcag tggaaagagg\n",
      "     2041 gacccatgaa gaattactgg aaaggaaagg tgtttacttc actctagtga ctttgcaaag\n",
      "     2101 ccagggaaat caagctctta atgaagagga cataaaggat gcaactgaag atgacatgct\n",
      "     2161 tgcgaggacc tttagcagag ggagctacca ggatagttta agggcttcca tccggcaacg\n",
      "     2221 ctccaagtct cagctttctt acctggtgca cgaacctcca ttagctgttg tagatcataa\n",
      "     2281 gtctacctat gaagaagata gaaaggacaa ggacattcct gtgcaggaag aagttgaacc\n",
      "     2341 tgccccagtt aggaggattc tgaaattcag tgctccagaa tggccctaca tgctggtagg\n",
      "     2401 gtctgtgggt gcagctgtga acgggacagt cacacccttg tatgcctttt tattcagcca\n",
      "     2461 gattcttggg actttttcaa ttcctgataa agaggaacaa aggtcacaga tcaatggtgt\n",
      "     2521 gtgcctactt tttgtagcaa tgggctgtgt atctcttttc acccaatttc tacagggata\n",
      "     2581 tgcctttgct aaatctgggg agctcctaac aaaaaggcta cgtaaatttg gtttcagggc\n",
      "     2641 aatgctgggg caagatattg cctggtttga tgacctcaga aatagccctg gagcattgac\n",
      "     2701 aacaagactt gctacagatg cttcccaagt tcaaggggct gccggctctc agatcgggat\n",
      "     2761 gatagtcaat tccttcacta acgtcactgt ggccatgatc attgccttct cctttagctg\n",
      "     2821 gaagctgagc ctggtcatct tgtgcttctt ccccttcttg gctttatcag gagccacaca\n",
      "     2881 gaccaggatg ttgacaggat ttgcctctcg agataagcag gccctggaga tggtgggaca\n",
      "     2941 gattacaaat gaagccctca gtaacatccg cactgttgct ggaattggaa aggagaggcg\n",
      "     3001 gttcattgaa gcacttgaga ctgagctgga gaagcccttc aagacagcca ttcagaaagc\n",
      "     3061 caatatttac ggattctgct ttgcctttgc ccagtgcatc atgtttattg cgaattctgc\n",
      "     3121 ttcctacaga tatggaggtt acttaatctc caatgagggg ctccatttca gctatgtgtt\n",
      "     3181 cagggtgatc tctgcagttg tactgagtgc aacagctctt ggaagagcct tctcttacac\n",
      "     3241 cccaagttat gcaaaagcta aaatatcagc tgcacgcttt tttcaactgc tggaccgaca\n",
      "     3301 acccccaatc agtgtataca atactgcagg tgaaaaatgg gacaacttcc aggggaagat\n",
      "     3361 tgattttgtt gattgtaaat ttacatatcc ttctcgacct gactcgcaag ttctgaatgg\n",
      "     3421 tctctcagtg tcgattagtc cagggcagac actggcgttt gttgggagca gtggatgtgg\n",
      "     3481 caaaagcact agcattcagc tgttggaacg tttctatgat cctgatcaag ggaaggtgat\n",
      "     3541 gatagatggt catgacagca aaaaagtaaa tgtccagttc ctccgctcaa acattggaat\n",
      "     3601 tgtttcccag gaaccagtgt tgtttgcctg tagcataatg gacaatatca agtatggaga\n",
      "     3661 caacaccaaa gaaattccca tggaaagagt catagcagct gcaaaacagg ctcagctgca\n",
      "     3721 tgattttgtc atgtcactcc cagagaaata tgaaactaac gttgggtccc aggggtctca\n",
      "     3781 actctctaga ggggagaaac aacgcattgc tattgctcgg gccattgtac gagatcctaa\n",
      "     3841 aatcttgcta ctagatgaag ccacttctgc cttagacaca gaaagtgaaa agacggtgca\n",
      "     3901 ggttgctcta gacaaagcca gagagggtcg gacctgcatt gtcattgccc atcgcttgtc\n",
      "     3961 caccatccag aacgcggata tcattgctgt catggcacag ggggtggtga ttgaaaaggg\n",
      "     4021 gacccatgaa gaactgatgg cccaaaaagg agcctactac aaactagtca ccactggatc\n",
      "     4081 ccccatcagt tgacccaatg caagaatctc agacacacat gacgcaccag ttacaggggt\n",
      "     4141 tgtttttaaa gaaaaaaaca atcccagcag gagggattgc tgggattgtt ttttctttaa\n",
      "     4201 agaagaatgt taatatttta cttttacagt cattttccta catcggaatc caagctaatt\n",
      "     4261 tctaatggcc ttccataata attctgcttt agatgtgtat acagaaaatg aaagaaacta\n",
      "     4321 gggtccatat gagggaaaac ccaatgtcaa gtggcagctc agccaccact cagtgcttct\n",
      "     4381 ctgtgcagga gccagtcctg attaatatgt gggaattagt gagacatcag ggagtaagtg\n",
      "     4441 acactttgaa ctcctcaagg gcagagaact gtctttcatt tttgaaccct cggtgtacac\n",
      "     4501 agaggcgggt ctataacagg caatcaacaa acgtttcttg agctagacca aggtcagatt\n",
      "     4561 tgaaaagaac agaaggactg aagaccagct gtgtttctta actaaatttg tctttcaagt\n",
      "     4621 gaaaccagct tccttcatct ctaaggctaa ggatagggaa agggtggatg ctctcaggct\n",
      "     4681 gagggaggca gaaagggaaa gtattagcat gagctttcca gttagggctg ttgatttatg\n",
      "     4741 ctttaacttc agagtgagtg taggggtggt gatgctacca ttactgtgag gacctaccag\n",
      "     4801 tgtggctgga gcagggactc tctcccaggc cttttactcc tcagcacctc cctgcatact\n",
      "     4861 gattgttgtt tttagtttct gtgaaattat attcatgaaa tgaaaatagc gcattttact\n",
      "     4921 ttgctgtagt ttcataaggt tttatacaaa aaagcaagta aatatggcag aaaagcactc\n",
      "     4981 atttgcccct gctccctcaa aacaccacag aatgacatag aactaaaggc ggcaggaatc\n",
      "     5041 tacaagaatg aagaaaacac agtgatgcca cctgcaaaat cttgggagcc agaaagcaaa\n",
      "     5101 tggacaattg ataatagagt tacaagatga gagaaaacaa aaatgtaacc tgttagttgg\n",
      "     5161 gggagcctag aaacatcctg ttttgtacca cagaccccta gaaagtttca agatgtaaaa\n",
      "     5221 acactggatc cttctggaag gaggagacaa ggggacagag ggactgaaga cagaagaatg\n",
      "     5281 gaccaaaagc ctgtatggaa acagaattgc agagccccgc ctgcagcagg atggctgcct\n",
      "     5341 ttccccagtt ccagcgagaa actgcatact ccctctctga ggaggctcac agggaggttt\n",
      "     5401 gcacttagag acacaagatg aagttgaagg ggcagctaac atacaagaga cagggggatt\n",
      "     5461 gaatgtaaag ctgtgtatga acagaagaac tcccagcccc tctcttctgg caggagattg\n",
      "     5521 aagaatgatt ttctggggaa attggccaat cttagaaaag aggtcgggcc aggcgctgtg\n",
      "     5581 gctcactcct gtaatcccag cactttggga ggccaaggcg ggcggatcat gaggtcgaga\n",
      "     5641 gattgagacc atcctggcta acatggtgaa accccgtctc tactaaaaat acaaaaaaat\n",
      "     5701 tagccgggcg tggtggcggg cgcctgtagt cccagctact caggaggctg aggcaggaga\n",
      "     5761 atggcgtgaa cccgggaggt ggagcttgca gtgagccgag atcgcgccac tgcactccag\n",
      "     5821 cctgggcgac agagcgaaaa aaaaaaaaaa agaaaaagaa aaagaaaaga ggtcaaggac\n",
      "     5881 tccgtccttg gaatcctaag aaaattttcc agccgtatta cccttctatg aagcccacct\n",
      "     5941 gtcaaccaac aagcacccac tcgatcagag cttccccagg ctttttggtg tctcctcctt\n",
      "     6001 gcatgggaat tgacttccaa ggaccaccag acactgagga agtattttaa catataaagc\n",
      "     6061 aaaagcaaca atagggcagc tggagaaagg aaattagaag taacagagcc aatgcagtga\n",
      "     6121 ttagaaaaac actcaaaaaa tggtaataaa tgtgttcaat gggtcaagag aacatatttc\n",
      "     6181 catctattta aataaaaaca ggaatcaata aaagtgaaca tacaaaaaag agctcttgtc\n",
      "     6241 acagaaatga aaaccttggg agcaggactg cacccacggt tcccaccaac ctatcctgcc\n",
      "     6301 atcatgtttt ctccctactc cagcttcctc ccaagctcac tctacgtaga tggtttttct\n",
      "     6361 tcccttagcc aacaaacgaa attctgccta taaattaagc caggacacta ggatatggag\n",
      "     6421 gtatattatt tatgtctctt ttccagtgtt tcctggtata taacagcaaa gatggtttag\n",
      "     6481 caagttaact ggtcaggcca gaattcttga tggttgccaa gtcaggaggc agacggtgaa\n",
      "     6541 ggaatgcatt ctggttatga aaaatggcaa tgacgagtaa gttgcagagt aaagatgcct\n",
      "     6601 tttagaggaa attaaggttt gcaataaatg catgctaatc ctctaatttt gatgaaagac\n",
      "     6661 taaagctctt gttttggttt gcatttcaaa gagcaagagc ataggctctt gtgctgggag\n",
      "     6721 gtggccagtt tcctggaaag gaatttatgg agtctgaaag aggaattagt acaaattata\n",
      "     6781 ttttcaaata agatacttga aagttattga tgacagggaa aagattgtct aaagagggct\n",
      "     6841 tgaaattggg gaaataattg aggctcagtg acaaaggaga agattacaac ttcaaaaatg\n",
      "     6901 aataaataaa taacattgca tgtttatttt acaa\n",
      "//\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# Procurar um tag meta com um determinado atributo\n",
    "\n",
    "url = f\"https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id={id}&db=nuccore&report=genbank&conwithfeat=on&hide-cdd=on&retmode=text&maxdownloadsize=5000000\"\n",
    "\n",
    "r2 = requests.get( url )\n",
    "print(r2.text)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Criamos um ficheiro no formato gb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "O ID na base de dados Nucleotide é NM_003742.\n",
      "Resultados gravados no ficheiro NM_003742.gb.\n"
     ]
    }
   ],
   "source": [
    "def save_genbank(text):\n",
    "\n",
    "    \"\"\"\n",
    "    Função que recebe a informação de um gene do ncbi e guarda num ficheiro formato gb\n",
    "    \"\"\"\n",
    "    \n",
    "    match = re.search(r'LOCUS\\s+(.*?)\\s+\\b', text)\n",
    "\n",
    "    if match:\n",
    "        nuccore_id = match.group(1)\n",
    "        print(f'O ID na base de dados Nucleotide é {nuccore_id}.')\n",
    "\n",
    "        filename = f'{nuccore_id}.gb'\n",
    "        with open(filename,'w',encoding='utf-8') as gb_file:\n",
    "            gb_file.write(text)\n",
    "            print(f'Resultados gravados no ficheiro {filename}.')\n",
    "\n",
    "save_genbank(r2.text)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [],
   "source": [
    "def parse_genbank(locus):\n",
    "    \n",
    "    \"\"\"\n",
    "    Extração de alguns dados do registo Genbank e retorna um tuplo com os dados de interesse: \n",
    "    \"id\", \"organismo\" e \"sequência\"\n",
    "    \"\"\"\n",
    "\n",
    "    i = re.match(r'LOCUS\\s+(\\w+)', locus)\n",
    "    if i:\n",
    "        id = i.group(1)\n",
    "    organism = \"\"\n",
    "    o = re.search(r'SOURCE\\s+.+', locus)\n",
    "    if o:\n",
    "        s = re.match(r'SOURCE\\s+(.+)', o[0] )\n",
    "        if s:\n",
    "            organism = s.group(1)\n",
    "    sequencia = \"\"\n",
    "    existe = re.findall(r'^\\s+\\d+ [actg ]+', locus, re.MULTILINE )\n",
    "    if existe:\n",
    "        for linha in existe:\n",
    "            m = re.match( r'\\s+\\d+ (.+)', linha, re.DOTALL )\n",
    "           \n",
    "            sequencia = sequencia + re.sub(r'\\s+', '', m.group(1) )\n",
    "    return (id, organism, sequencia)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "População de bases de dados com os resultados de múltiplas pesquisas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [],
   "source": [
    "DataBase = pymysql.connect(\n",
    "   host =\"127.0.0.1\",\n",
    "   user =\"DuarteVelho1\",\n",
    "   password =\"123duarte\",\n",
    "    database =\"duartetrabalhos\"\n",
    ")\n",
    "\n",
    "# Criação de um cursor para executar comandos SQL\n",
    "Cursor = DataBase.cursor()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 50,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Parâmetros para a criação da tabela\n",
    "TableName =\"\"\"CREATE TABLE IF NOT EXISTS genbank\n",
    "    (\n",
    "    locusid varchar(255) PRIMARY KEY, \n",
    "    dnasource text, \n",
    "    dnasequence LONGTEXT\n",
    "    );\n",
    "\"\"\"\n",
    "\n",
    "# Executamos os comandos com recurso ao cursor\n",
    "Cursor.execute(TableName)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\Utilizador\\AppData\\Local\\Temp\\ipykernel_4476\\1056781267.py:1: UserWarning: pandas only supports SQLAlchemy connectable (engine/connection) or database string URI or sqlite3 DBAPI2 connection. Other DBAPI2 objects are not tested. Please consider using SQLAlchemy.\n",
      "  tabela = pd.read_sql(\"SELECT * FROM genbank\",DataBase)\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>locusid</th>\n",
       "      <th>dnasource</th>\n",
       "      <th>dnasequence</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NM_001159694</td>\n",
       "      <td>Homo sapiens (human)</td>\n",
       "      <td>acattcactacaccttttccatttgctaataaggccctgccaggct...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>NM_003742</td>\n",
       "      <td>Homo sapiens (human)</td>\n",
       "      <td>agaatgatgaaaaccgaggttggaaaaggttgtgaaaccttttaac...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NM_153603</td>\n",
       "      <td>Homo sapiens (human)</td>\n",
       "      <td>gagggtcattcccagccgcaaactgagtgcgctgagcggggaagcg...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>NM_198510</td>\n",
       "      <td>Homo sapiens (human)</td>\n",
       "      <td>agatcttctggatgtgaacaacagatccaggccagaggtggcatca...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        locusid             dnasource  \\\n",
       "0  NM_001159694  Homo sapiens (human)   \n",
       "1     NM_003742  Homo sapiens (human)   \n",
       "2     NM_153603  Homo sapiens (human)   \n",
       "3     NM_198510  Homo sapiens (human)   \n",
       "\n",
       "                                         dnasequence  \n",
       "0  acattcactacaccttttccatttgctaataaggccctgccaggct...  \n",
       "1  agaatgatgaaaaccgaggttggaaaaggttgtgaaaccttttaac...  \n",
       "2  gagggtcattcccagccgcaaactgagtgcgctgagcggggaagcg...  \n",
       "3  agatcttctggatgtgaacaacagatccaggccagaggtggcatca...  "
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tabela = pd.read_sql(\"SELECT * FROM genbank\",DataBase)\n",
    "tabela"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [],
   "source": [
    "sql = \"INSERT IGNORE INTO genbank (locusid, dnasource, dnasequence) VALUES (%s, %s, %s)\"\n",
    "val = parse_genbank(r2.text)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0 record inserted.\n"
     ]
    }
   ],
   "source": [
    "Cursor.execute(sql, val)\n",
    "\n",
    "DataBase.commit()  # Executamos as modificações, fazendo commit.\n",
    "\n",
    "print(Cursor.rowcount, \"record inserted.\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\Utilizador\\AppData\\Local\\Temp\\ipykernel_4476\\2230997112.py:1: UserWarning: pandas only supports SQLAlchemy connectable (engine/connection) or database string URI or sqlite3 DBAPI2 connection. Other DBAPI2 objects are not tested. Please consider using SQLAlchemy.\n",
      "  tabela = pd.read_sql(\"SELECT locusid, length(dnasequence) as comprimento FROM genbank\",DataBase)\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>locusid</th>\n",
       "      <th>comprimento</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NM_001159694</td>\n",
       "      <td>3927</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>NM_003742</td>\n",
       "      <td>6934</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NM_153603</td>\n",
       "      <td>2935</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>NM_198510</td>\n",
       "      <td>4964</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        locusid  comprimento\n",
       "0  NM_001159694         3927\n",
       "1     NM_003742         6934\n",
       "2     NM_153603         2935\n",
       "3     NM_198510         4964"
      ]
     },
     "execution_count": 54,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tabela = pd.read_sql(\"SELECT locusid, length(dnasequence) as comprimento FROM genbank\",DataBase)\n",
    "tabela"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_genbank(gene):\n",
    "\n",
    "    \"\"\"\n",
    "    Vai buscar o registo a partir do nome do gene\n",
    "    \"\"\"\n",
    "    \n",
    "    url = f'https://www.ncbi.nlm.nih.gov/nuccore/{gene}'\n",
    "    r = requests.get(url)\n",
    "    soup = BeautifulSoup(r.content, 'html.parser')\n",
    "    id = soup.find_all('meta',{'name':'ncbi_uidlist'})[0].attrs['content']\n",
    "    url = f\"https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id={id}&db=nuccore&report=genbank&conwithfeat=on&hide-cdd=on&retmode=text&maxdownloadsize=5000000\"\n",
    "    r2 = requests.get(url)\n",
    "    return r2.text"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "O ID na base de dados Nucleotide é NM_153603.\n",
      "Resultados gravados no ficheiro NM_153603.gb.\n",
      "O ID na base de dados Nucleotide é NM_001159694.\n",
      "Resultados gravados no ficheiro NM_001159694.gb.\n",
      "O ID na base de dados Nucleotide é NM_198510.\n",
      "Resultados gravados no ficheiro NM_198510.gb.\n"
     ]
    }
   ],
   "source": [
    "genes = [\n",
    "    'NM_153603',\n",
    "    'NM_001159694',\n",
    "    'NM_198510'\n",
    "]\n",
    "\n",
    "# Verificamos todos os genes utilizando um ciclo for com recurso ao módulo time\n",
    "# chamamos a função save_genbank que criou os ficheiros gb para o respetivo gene\n",
    "# para não sobrecarregar o servidor\n",
    "\n",
    "vals = []\n",
    "for gene in genes:\n",
    "\n",
    "    content = get_genbank(gene)\n",
    "    save_genbank(content)\n",
    "    vals.append(parse_genbank(content))\n",
    "    time.sleep(5)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Guardar os restantes genes na BD"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [],
   "source": [
    "sql = \"INSERT IGNORE INTO genbank (locusid, dnasource, dnasequence) VALUES (%s, %s, %s)\"\n",
    "for val in vals:\n",
    "    Cursor.execute(sql, val)\n",
    "DataBase.commit()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Criar uma tabela para os restantes genes:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\Utilizador\\AppData\\Local\\Temp\\ipykernel_4476\\2230997112.py:1: UserWarning: pandas only supports SQLAlchemy connectable (engine/connection) or database string URI or sqlite3 DBAPI2 connection. Other DBAPI2 objects are not tested. Please consider using SQLAlchemy.\n",
      "  tabela = pd.read_sql(\"SELECT locusid, length(dnasequence) as comprimento FROM genbank\",DataBase)\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>locusid</th>\n",
       "      <th>comprimento</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NM_001159694</td>\n",
       "      <td>3927</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>NM_003742</td>\n",
       "      <td>6934</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NM_153603</td>\n",
       "      <td>2935</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>NM_198510</td>\n",
       "      <td>4964</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        locusid  comprimento\n",
       "0  NM_001159694         3927\n",
       "1     NM_003742         6934\n",
       "2     NM_153603         2935\n",
       "3     NM_198510         4964"
      ]
     },
     "execution_count": 58,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tabela = pd.read_sql(\"SELECT locusid, length(dnasequence) as comprimento FROM genbank\",DataBase)\n",
    "tabela"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Se quisermos todas as colunas completas da tabela:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\Utilizador\\AppData\\Local\\Temp\\ipykernel_4476\\1056781267.py:1: UserWarning: pandas only supports SQLAlchemy connectable (engine/connection) or database string URI or sqlite3 DBAPI2 connection. Other DBAPI2 objects are not tested. Please consider using SQLAlchemy.\n",
      "  tabela = pd.read_sql(\"SELECT * FROM genbank\",DataBase)\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>locusid</th>\n",
       "      <th>dnasource</th>\n",
       "      <th>dnasequence</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NM_001159694</td>\n",
       "      <td>Homo sapiens (human)</td>\n",
       "      <td>acattcactacaccttttccatttgctaataaggccctgccaggct...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>NM_003742</td>\n",
       "      <td>Homo sapiens (human)</td>\n",
       "      <td>agaatgatgaaaaccgaggttggaaaaggttgtgaaaccttttaac...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NM_153603</td>\n",
       "      <td>Homo sapiens (human)</td>\n",
       "      <td>gagggtcattcccagccgcaaactgagtgcgctgagcggggaagcg...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>NM_198510</td>\n",
       "      <td>Homo sapiens (human)</td>\n",
       "      <td>agatcttctggatgtgaacaacagatccaggccagaggtggcatca...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        locusid             dnasource  \\\n",
       "0  NM_001159694  Homo sapiens (human)   \n",
       "1     NM_003742  Homo sapiens (human)   \n",
       "2     NM_153603  Homo sapiens (human)   \n",
       "3     NM_198510  Homo sapiens (human)   \n",
       "\n",
       "                                         dnasequence  \n",
       "0  acattcactacaccttttccatttgctaataaggccctgccaggct...  \n",
       "1  agaatgatgaaaaccgaggttggaaaaggttgtgaaaccttttaac...  \n",
       "2  gagggtcattcccagccgcaaactgagtgcgctgagcggggaagcg...  \n",
       "3  agatcttctggatgtgaacaacagatccaggccagaggtggcatca...  "
      ]
     },
     "execution_count": 59,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tabela = pd.read_sql(\"SELECT * FROM genbank\",DataBase)\n",
    "tabela"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Fecho do cursos e conexão à base de dados"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "metadata": {},
   "outputs": [],
   "source": [
    "Cursor.close()\n",
    "DataBase.close()"
   ]
  }
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