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  1. {
  2.  "cells": [
  3.   {
  4.    "cell_type": "markdown",
  5.    "metadata": {},
  6.    "source": [
  7.     "## Jupyter notebook\n",
  8.     "\n",
  9.     "..."
  10.    ]
  11.   },
  12.   {
  13.    "cell_type": "code",
  14.    "execution_count": 17,
  15.    "metadata": {},
  16.    "outputs": [],
  17.    "source": [
  18.     "from Bio import SeqIO"
  19.    ]
  20.   },
  21.   {
  22.    "cell_type": "code",
  23.    "execution_count": 18,
  24.    "metadata": {},
  25.    "outputs": [],
  26.    "source": [
  27.     "with open(\"test.gb\") as h:\n",
  28.     "    seq = SeqIO.read(h, format=\"gb\")"
  29.    ]
  30.   },
  31.   {
  32.    "cell_type": "code",
  33.    "execution_count": 19,
  34.    "metadata": {},
  35.    "outputs": [
  36.     {
  37.      "data": {
  38.       "text/plain": [
  39.        "SeqRecord(seq=Seq('GATC', IUPACAmbiguousDNA()), id='test', name='test', description='', dbxrefs=[])"
  40.       ]
  41.      },
  42.      "execution_count": 19,
  43.      "metadata": {},
  44.      "output_type": "execute_result"
  45.     }
  46.    ],
  47.    "source": [
  48.     "seq"
  49.    ]
  50.   },
  51.   {
  52.    "cell_type": "code",
  53.    "execution_count": 27,
  54.    "metadata": {},
  55.    "outputs": [
  56.     {
  57.      "name": "stdout",
  58.      "output_type": "stream",
  59.      "text": [
  60.       "LOCUS       test                       4 bp    ds-DNA  linear   UNK 10-JUL-2019\n",
  61.       "DEFINITION  .\n",
  62.       "ACCESSION   test\n",
  63.       "VERSION     test\n",
  64.       "KEYWORDS    .\n",
  65.       "SOURCE      \n",
  66.       "  ORGANISM  .\n",
  67.       "            .\n",
  68.       "COMMENT     \n",
  69.       "            \n",
  70.       "            ApEinfo:methylated:1\n",
  71.       "FEATURES             Location/Qualifiers\n",
  72.       "     misc_feature    2..3\n",
  73.       "                     /locus_tag=\"MyFeature\"\n",
  74.       "                     /label=\"MyFeature\"\n",
  75.       "                     /ApEinfo_label=\"MyFeature\"\n",
  76.       "                     /ApEinfo_fwdcolor=\"cyan\"\n",
  77.       "                     /ApEinfo_revcolor=\"green\"\n",
  78.       "                     /ApEinfo_graphicformat=\"arrow_data {{0 1 2 0 0 -1} {} 0}\n",
  79.       "                     width 5 offset 0\"\n",
  80.       "ORIGIN\n",
  81.       "        1 gatc\n",
  82.       "//\n",
  83.       "\n"
  84.      ]
  85.     }
  86.    ],
  87.    "source": [
  88.     "print(seq.format(\"gb\"))"
  89.    ]
  90.   },
  91.   {
  92.    "cell_type": "code",
  93.    "execution_count": 20,
  94.    "metadata": {},
  95.    "outputs": [
  96.     {
  97.      "data": {
  98.       "text/plain": [
  99.        "Bio.SeqRecord.SeqRecord"
  100.       ]
  101.      },
  102.      "execution_count": 20,
  103.      "metadata": {},
  104.      "output_type": "execute_result"
  105.     }
  106.    ],
  107.    "source": [
  108.     "type(seq)"
  109.    ]
  110.   },
  111.   {
  112.    "cell_type": "code",
  113.    "execution_count": 21,
  114.    "metadata": {},
  115.    "outputs": [],
  116.    "source": [
  117.     "from pydna.seqrecord import SeqRecord"
  118.    ]
  119.   },
  120.   {
  121.    "cell_type": "code",
  122.    "execution_count": 22,
  123.    "metadata": {},
  124.    "outputs": [],
  125.    "source": [
  126.     "seq2 = SeqRecord(str(seq.seq))"
  127.    ]
  128.   },
  129.   {
  130.    "cell_type": "code",
  131.    "execution_count": 23,
  132.    "metadata": {},
  133.    "outputs": [],
  134.    "source": [
  135.     "seq2.__dict__.update(seq.__dict__)"
  136.    ]
  137.   },
  138.   {
  139.    "cell_type": "code",
  140.    "execution_count": 24,
  141.    "metadata": {},
  142.    "outputs": [
  143.     {
  144.      "data": {
  145.       "text/plain": [
  146.        "pydna.seqrecord.SeqRecord"
  147.       ]
  148.      },
  149.      "execution_count": 24,
  150.      "metadata": {},
  151.      "output_type": "execute_result"
  152.     }
  153.    ],
  154.    "source": [
  155.     "type(seq2)"
  156.    ]
  157.   },
  158.   {
  159.    "cell_type": "code",
  160.    "execution_count": 25,
  161.    "metadata": {},
  162.    "outputs": [
  163.     {
  164.      "data": {
  165.       "text/plain": [
  166.        "+-----+---------------+-----+-----+-----+-----+--------------+------+\n",
  167.        "| Ft# | Label or Note | Dir | Sta | End | Len | type         | orf? |\n",
  168.        "+-----+---------------+-----+-----+-----+-----+--------------+------+\n",
  169.        "|   0 | L:MyFeature   | --> | 1   | 3   |   2 | misc_feature |  no  |\n",
  170.        "+-----+---------------+-----+-----+-----+-----+--------------+------+"
  171.       ]
  172.      },
  173.      "execution_count": 25,
  174.      "metadata": {},
  175.      "output_type": "execute_result"
  176.     }
  177.    ],
  178.    "source": [
  179.     "seq2.list_features()"
  180.    ]
  181.   },
  182.   {
  183.    "cell_type": "code",
  184.    "execution_count": null,
  185.    "metadata": {},
  186.    "outputs": [],
  187.    "source": []
  188.   }
  189.  ],
  190.  "metadata": {
  191.   "anaconda-cloud": {},
  192.   "kernelspec": {
  193.    "display_name": "Python [conda env:bjorn37]",
  194.    "language": "python",
  195.    "name": "conda-env-bjorn37-py"
  196.   },
  197.   "language_info": {
  198.    "codemirror_mode": {
  199.     "name": "ipython",
  200.     "version": 3
  201.    },
  202.    "file_extension": ".py",
  203.    "mimetype": "text/x-python",
  204.    "name": "python",
  205.    "nbconvert_exporter": "python",
  206.    "pygments_lexer": "ipython3",
  207.    "version": "3.7.3"
  208.   }
  209.  },
  210.  "nbformat": 4,
  211.  "nbformat_minor": 2
  212. }
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