Create and manipulate molecules with PyRNA

gistfile1.py

{
 "metadata": {
  "name": "Create and manipulate molecules."
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": "Create molecules from scratch"
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "PyRNA allows you to construct easily DNA and RNA molecules. An RNA molecule will automatically convert T residues into U."
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "from pyrna.features import DNA, RNA\nrna = RNA(name = 'my_rna', sequence = 'GGGGGATTAACCCC')\nprint \"%s: %s\"%(rna.name, rna.sequence)\ndna = DNA(name = 'my_dna', sequence = 'GGGGGATTAACCCC')\nprint \"%s: %s\"%(dna.name, dna.sequence)",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "my_rna: GGGGGAUUAACCCC\nmy_dna: GGGGGATTAACCCC\n"
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "RNA and DNA molecules can return their length, are slicable and iterable:"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "print \"slice: %s\"%rna[0:2]\nprint \"length: %i\"%len(rna)",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "slice: GG\nlength: 14\n"
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "You can easily get a single residue:"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "print rna[3]",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "G\n"
      }
     ],
     "prompt_number": 8
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "The sequence can be easily changed by adding a new string at the end:"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "rna +'AAA'\nprint rna.sequence",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "GGGGGAUUAACCCCAAA\n"
      }
     ],
     "prompt_number": 13
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "Or by removing some residues from the end:"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "rna-3\nprint rna.sequence",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "GGGGGAUUAACCCC\n"
      }
     ],
     "prompt_number": 12
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "An RNA molecule is iterable over its primary sequence:"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "for index, residue in enumerate(rna):\n    print \"residue n%i: %s\"%(index+1, residue)",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "residue n1: G\nresidue n2: G\nresidue n3: G\nresidue n4: G\nresidue n5: G\nresidue n6: A\nresidue n7: U\nresidue n8: U\nresidue n9: A\nresidue n10: A\nresidue n11: C\nresidue n12: C\nresidue n13: C\nresidue n14: C\n"
      }
     ],
     "prompt_number": 6
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": "Create molecules from files"
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "With PyRNA, an object pyrna.features.TertiaryStructure is made with a single molecular chain. Since a PDB file can contains several molecules, the function parse_pdb() returns a list of such objects."
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "h = open('data/1ehz.pdb')\npdb_content = h.read()\nh.close()\n\nfrom pyrna.parsers import parse_pdb\ntertiary_structures = parse_pdb(pdb_content)",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 16
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "RNA molecules extracted from PDB files can contain modified residues. PyRNA converts them automatically into unmodified residues, and stores the modification in a dictionary."
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "for ts in tertiary_structures:\n    print ts.rna.name\n    print ts.rna.sequence\n    print ts.rna.modified_residues",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "A\nGCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA\n[('2MG', 10), ('H2U', 16), ('H2U', 17), ('M2G', 26), ('OMC', 32), ('OMG', 34), ('YYG', 37), ('PSU', 39), ('5MC', 40), ('7MG', 46), ('5MC', 49), ('5MU', 54), ('PSU', 55), ('1MA', 58)]\n"
      }
     ],
     "prompt_number": 10
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "If you want to parse a FASTA file, you have to precise the type of molecules stored. DNA molecules are faster to create since PyRNA will not try to identify modified residues."
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "h = open('data/telomerases.fasta')\nfasta_content = h.read()\nh.close()\n\nfrom pyrna.parsers import parse_fasta\n#the default type is RNA\nfor rna in parse_fasta(fasta_content):\n    print \"sequence of %s:\"%rna.name\n    print \"%s\\n\"%rna.sequence",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "sequence of telomerase 1:\nAGUUUCUCGAUAAUUGAUCUGUAGAAUCUGUCAAGCAAAACCCCAAAACCUUACACUGAGAGCAUUUAGCCUGAUUACUCUUUAAAUCAAAUCAGGCAAUAGAGAGAAACUCGAGAGGUGAAAACCCCACAGCAUUCUGAAAUGUAUUUGGGAGUAAUCUCAUAUUAGUUUGCUGUCCUCUCAUCUUUU\n\nsequence of telomerase 2:\nAUCCCCGCAAAUUCAUUCUGUUUGCAUUCAAACAGUCAUUCAACCCCAAAAAUCUAGACCAAAUAUUGUCUUCCCUUCUUGGCACAAACAAAGAAGAGACGCGGGAUAAAGAUACUCCGACGAUUGAUACAAUAUUUAUCAACGGGAGGUCUUACUUUU\n\nsequence of telomerase 3:\nUACCUCCUGUGGAUCCAUUCAGGAUUAAUGAAAUCCUGUCAUUCAACCCCAAAAAUCUUGUCAAAUUAUUGCCUCGUCUUUUGGGCACAAACAAAAGUCACGCAGGAGGUUCAGACAUUCGACAUAAGAUACACUAUUUAUCUUAUGGAAGGUCUAGUUUUU\n\n"
      }
     ],
     "prompt_number": 21
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "An object RNA will automatically convert T residues into U."
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "h = open('data/ft3100_from_FANTOM3_project.fasta')\nfasta_content = h.read()\nh.close()\n\nfor dna in parse_fasta(fasta_content, 'DNA'):\n    print \"sequence as a DNA:\"\n    print \"%s\\n\"%dna.sequence\n\nfor rna in parse_fasta(fasta_content):\n    print \"sequence as an RNA:\"\n    print rna.sequence",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "sequence as a DNA:\nTAACAATCTGCTGAAAGGTACCGTCGGAGGGAGCTTTGTTGCCAGCGCCAGAAACGCCGGTTTAACCAGCGCCGAAGTGAGCGCAGTGATTAAAGCCATGCAGTGGCAAATGGATTTCCGCAAACTGAAAAAAGGCGATGAATTTGCGGT\n\nsequence as an RNA:\nUAACAAUCUGCUGAAAGGUACCGUCGGAGGGAGCUUUGUUGCCAGCGCCAGAAACGCCGGUUUAACCAGCGCCGAAGUGAGCGCAGUGAUUAAAGCCAUGCAGUGGCAAAUGGAUUUCCGCAAACUGAAAAAAGGCGAUGAAUUUGCGGU\n"
      }
     ],
     "prompt_number": 14
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "DNA and RNA objects have a rich textual representation in IPython notebooks. "
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "parse_fasta(fasta_content)[0]",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "html": "<pre>1\t<font color=\"green\">U</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"orange\">C</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"green\">U</font><font color=\"orange\">C</font><font color=\"green\">U</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"green\">U</font><font color=\"red\">G</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"red\">G</font><font color=\"red\">G</font><font color=\"green\">U</font><font color=\"blue\">A</font><font color=\"orange\">C</font><font color=\"orange\">C</font><font color=\"red\">G</font><font color=\"green\">U</font><font color=\"orange\">C</font><font color=\"red\">G</font><font color=\"red\">G</font><font color=\"blue\">A</font><font color=\"red\">G</font><font color=\"red\">G</font><font color=\"red\">G</font><font color=\"blue\">A</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"green\">U</font><font color=\"green\">U</font><font color=\"green\">U</font><font color=\"red\">G</font><font color=\"green\">U</font><font color=\"green\">U</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"orange\">C</font><font color=\"blue\">A</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"orange\">C</font><font color=\"blue\">A</font><font color=\"red\">G</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"orange\">C</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"orange\">C</font><font color=\"red\">G</font><font color=\"red\">G</font>\n61\t<font color=\"green\">U</font><font color=\"green\">U</font><font color=\"green\">U</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"orange\">C</font><font color=\"orange\">C</font><font color=\"blue\">A</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"orange\">C</font><font color=\"red\">G</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"red\">G</font><font color=\"green\">U</font><font color=\"red\">G</font><font color=\"blue\">A</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"blue\">A</font><font color=\"red\">G</font><font color=\"green\">U</font><font color=\"red\">G</font><font color=\"blue\">A</font><font color=\"green\">U</font><font color=\"green\">U</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"orange\">C</font><font color=\"blue\">A</font><font color=\"green\">U</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"blue\">A</font><font color=\"red\">G</font><font color=\"green\">U</font><font color=\"red\">G</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"green\">U</font><font color=\"red\">G</font><font color=\"red\">G</font><font color=\"blue\">A</font><font color=\"green\">U</font><font color=\"green\">U</font><font color=\"green\">U</font><font color=\"orange\">C</font><font color=\"orange\">C</font><font color=\"red\">G</font>\n121\t<font color=\"orange\">C</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"orange\">C</font><font color=\"green\">U</font><font color=\"red\">G</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"red\">G</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"red\">G</font><font color=\"blue\">A</font><font color=\"green\">U</font><font color=\"red\">G</font><font color=\"blue\">A</font><font color=\"blue\">A</font><font color=\"green\">U</font><font color=\"green\">U</font><font color=\"green\">U</font><font color=\"red\">G</font><font color=\"orange\">C</font><font color=\"red\">G</font><font color=\"red\">G</font><font color=\"green\">U</font>\n</pre>",
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 15,
       "text": "<pyrna.features.RNA instance at 0x109c5be60>"
      }
     ],
     "prompt_number": 15
    },
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": "Create molecules from databases"
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "You can load 3D structures directly from the Protein Databank"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "from pyrna.db import PDB\npdb = PDB()\npdb_content = pdb.get_entry('1GID')",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 6
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "With PyRNA, a pyrna.features.TertiaryStructure object is made with a single molecular chain. Since a PDB file can contains several molecules, the function parse_pdb returns a list of pyrna.features.TertiaryStructure."
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "from pyrna.parsers import parse_pdb\n\nfor tertiary_structure in parse_pdb(pdb_content):\n    print \"molecular chain %s: %s\"%(tertiary_structure.rna.name, tertiary_structure.rna.sequence)",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "molecular chain A: GAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCACGCAGCCAAGUCCUAAGUCAACAGAUCUUCUGUUGAUAUGGAUGCAGUUC\nmolecular chain B: GAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCACGCAGCCAAGUCCUAAGUCAACAGAUCUUCUGUUGAUAUGGAUGCAGUUC\n"
      }
     ],
     "prompt_number": 10
    }
   ],
   "metadata": {}
  }
 ]
}