{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Jupyter notebook\n",
    "\n",
    "..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "from Bio import SeqIO"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(\"test.gb\") as h:\n",
    "    seq = SeqIO.read(h, format=\"gb\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "SeqRecord(seq=Seq('GATC', IUPACAmbiguousDNA()), id='test', name='test', description='', dbxrefs=[])"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "seq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "LOCUS       test                       4 bp    ds-DNA  linear   UNK 10-JUL-2019\n",
      "DEFINITION  .\n",
      "ACCESSION   test\n",
      "VERSION     test\n",
      "KEYWORDS    .\n",
      "SOURCE      \n",
      "  ORGANISM  .\n",
      "            .\n",
      "COMMENT     \n",
      "            \n",
      "            ApEinfo:methylated:1\n",
      "FEATURES             Location/Qualifiers\n",
      "     misc_feature    2..3\n",
      "                     /locus_tag=\"MyFeature\"\n",
      "                     /label=\"MyFeature\"\n",
      "                     /ApEinfo_label=\"MyFeature\"\n",
      "                     /ApEinfo_fwdcolor=\"cyan\"\n",
      "                     /ApEinfo_revcolor=\"green\"\n",
      "                     /ApEinfo_graphicformat=\"arrow_data {{0 1 2 0 0 -1} {} 0}\n",
      "                     width 5 offset 0\"\n",
      "ORIGIN\n",
      "        1 gatc\n",
      "//\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(seq.format(\"gb\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Bio.SeqRecord.SeqRecord"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "type(seq)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pydna.seqrecord import SeqRecord"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "seq2 = SeqRecord(str(seq.seq))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "seq2.__dict__.update(seq.__dict__)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "pydna.seqrecord.SeqRecord"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "type(seq2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "+-----+---------------+-----+-----+-----+-----+--------------+------+\n",
       "| Ft# | Label or Note | Dir | Sta | End | Len | type         | orf? |\n",
       "+-----+---------------+-----+-----+-----+-----+--------------+------+\n",
       "|   0 | L:MyFeature   | --> | 1   | 3   |   2 | misc_feature |  no  |\n",
       "+-----+---------------+-----+-----+-----+-----+--------------+------+"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "seq2.list_features()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "anaconda-cloud": {},
  "kernelspec": {
   "display_name": "Python [conda env:bjorn37]",
   "language": "python",
   "name": "conda-env-bjorn37-py"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}