12_The_BioPython_Project.ipynb

{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# https://biopython.org/\n",
    "# https://biopython.org/wiki/Documentation\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Requirement already satisfied: biopython in c:\\users\\ijaz ali jin\\appdata\\local\\programs\\python\\python311\\lib\\site-packages (1.81)Note: you may need to restart the kernel to use updated packages.\n",
      "\n",
      "Requirement already satisfied: numpy in c:\\users\\ijaz ali jin\\appdata\\local\\programs\\python\\python311\\lib\\site-packages (from biopython) (1.24.2)\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "[notice] A new release of pip available: 22.3.1 -> 23.1.2\n",
      "[notice] To update, run: python.exe -m pip install --upgrade pip\n"
     ]
    }
   ],
   "source": [
    "# pip install biopython\n",
    "# pip install biopython --upgrade \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1.81\n"
     ]
    }
   ],
   "source": [
    "import Bio # import the biopython package\n",
    "print(Bio.__version__) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Help on package Bio:\n",
      "\n",
      "NAME\n",
      "    Bio - Collection of modules for dealing with biological data in Python.\n",
      "\n",
      "DESCRIPTION\n",
      "    The Biopython Project is an international association of developers\n",
      "    of freely available Python tools for computational molecular biology.\n",
      "    \n",
      "    https://biopython.org\n",
      "\n",
      "PACKAGE CONTENTS\n",
      "    Affy (package)\n",
      "    Align (package)\n",
      "    AlignIO (package)\n",
      "    Alphabet (package)\n",
      "    Application (package)\n",
      "    Blast (package)\n",
      "    CAPS (package)\n",
      "    Cluster (package)\n",
      "    Compass (package)\n",
      "    Data (package)\n",
      "    Emboss (package)\n",
      "    Entrez (package)\n",
      "    ExPASy (package)\n",
      "    File\n",
      "    GenBank (package)\n",
      "    Geo (package)\n",
      "    Graphics (package)\n",
      "    HMM (package)\n",
      "    KEGG (package)\n",
      "    LogisticRegression\n",
      "    MarkovModel\n",
      "    MaxEntropy\n",
      "    Medline (package)\n",
      "    NMR (package)\n",
      "    NaiveBayes\n",
      "    Nexus (package)\n",
      "    PDB (package)\n",
      "    Pathway (package)\n",
      "    Phylo (package)\n",
      "    PopGen (package)\n",
      "    Restriction (package)\n",
      "    SCOP (package)\n",
      "    SVDSuperimposer (package)\n",
      "    SearchIO (package)\n",
      "    Seq\n",
      "    SeqFeature\n",
      "    SeqIO (package)\n",
      "    SeqRecord\n",
      "    SeqUtils (package)\n",
      "    Sequencing (package)\n",
      "    SwissProt (package)\n",
      "    TogoWS (package)\n",
      "    UniGene (package)\n",
      "    UniProt (package)\n",
      "    Wise (package)\n",
      "    _utils\n",
      "    bgzf\n",
      "    codonalign (package)\n",
      "    cpairwise2\n",
      "    kNN\n",
      "    motifs (package)\n",
      "    pairwise2\n",
      "    phenotype (package)\n",
      "\n",
      "CLASSES\n",
      "    builtins.Exception(builtins.BaseException)\n",
      "        MissingExternalDependencyError\n",
      "            MissingPythonDependencyError(MissingExternalDependencyError, builtins.ImportError)\n",
      "    builtins.ValueError(builtins.Exception)\n",
      "        StreamModeError\n",
      "    builtins.Warning(builtins.Exception)\n",
      "        BiopythonWarning\n",
      "            BiopythonDeprecationWarning\n",
      "            BiopythonExperimentalWarning\n",
      "            BiopythonParserWarning\n",
      "    \n",
      "    class BiopythonDeprecationWarning(BiopythonWarning)\n",
      "     |  Biopython deprecation warning.\n",
      "     |  \n",
      "     |  Biopython uses this warning instead of the built in DeprecationWarning\n",
      "     |  since those are ignored by default since Python 2.7.\n",
      "     |  \n",
      "     |  To silence all our deprecation warning messages, use:\n",
      "     |  \n",
      "     |  >>> import warnings\n",
      "     |  >>> from Bio import BiopythonDeprecationWarning\n",
      "     |  >>> warnings.simplefilter('ignore', BiopythonDeprecationWarning)\n",
      "     |  \n",
      "     |  Code marked as deprecated is likely to be removed in a future version\n",
      "     |  of Biopython. To avoid removal of this code, please contact the Biopython\n",
      "     |  developers via the mailing list or GitHub.\n",
      "     |  \n",
      "     |  Method resolution order:\n",
      "     |      BiopythonDeprecationWarning\n",
      "     |      BiopythonWarning\n",
      "     |      builtins.Warning\n",
      "     |      builtins.Exception\n",
      "     |      builtins.BaseException\n",
      "     |      builtins.object\n",
      "     |  \n",
      "     |  Data descriptors inherited from BiopythonWarning:\n",
      "     |  \n",
      "     |  __weakref__\n",
      "     |      list of weak references to the object (if defined)\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Methods inherited from builtins.Warning:\n",
      "     |  \n",
      "     |  __init__(self, /, *args, **kwargs)\n",
      "     |      Initialize self.  See help(type(self)) for accurate signature.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Static methods inherited from builtins.Warning:\n",
      "     |  \n",
      "     |  __new__(*args, **kwargs) from builtins.type\n",
      "     |      Create and return a new object.  See help(type) for accurate signature.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Methods inherited from builtins.BaseException:\n",
      "     |  \n",
      "     |  __delattr__(self, name, /)\n",
      "     |      Implement delattr(self, name).\n",
      "     |  \n",
      "     |  __getattribute__(self, name, /)\n",
      "     |      Return getattr(self, name).\n",
      "     |  \n",
      "     |  __reduce__(...)\n",
      "     |      Helper for pickle.\n",
      "     |  \n",
      "     |  __repr__(self, /)\n",
      "     |      Return repr(self).\n",
      "     |  \n",
      "     |  __setattr__(self, name, value, /)\n",
      "     |      Implement setattr(self, name, value).\n",
      "     |  \n",
      "     |  __setstate__(...)\n",
      "     |  \n",
      "     |  __str__(self, /)\n",
      "     |      Return str(self).\n",
      "     |  \n",
      "     |  add_note(...)\n",
      "     |      Exception.add_note(note) --\n",
      "     |      add a note to the exception\n",
      "     |  \n",
      "     |  with_traceback(...)\n",
      "     |      Exception.with_traceback(tb) --\n",
      "     |      set self.__traceback__ to tb and return self.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Data descriptors inherited from builtins.BaseException:\n",
      "     |  \n",
      "     |  __cause__\n",
      "     |      exception cause\n",
      "     |  \n",
      "     |  __context__\n",
      "     |      exception context\n",
      "     |  \n",
      "     |  __dict__\n",
      "     |  \n",
      "     |  __suppress_context__\n",
      "     |  \n",
      "     |  __traceback__\n",
      "     |  \n",
      "     |  args\n",
      "    \n",
      "    class BiopythonExperimentalWarning(BiopythonWarning)\n",
      "     |  Biopython experimental code warning.\n",
      "     |  \n",
      "     |  Biopython uses this warning for experimental code ('alpha' or 'beta'\n",
      "     |  level code) which is released as part of the standard releases to mark\n",
      "     |  sub-modules or functions for early adopters to test & give feedback.\n",
      "     |  \n",
      "     |  Code issuing this warning is likely to change (or even be removed) in\n",
      "     |  a subsequent release of Biopython. Such code should NOT be used for\n",
      "     |  production/stable code. It should only be used if:\n",
      "     |  \n",
      "     |  - You are running the latest release of Biopython, or ideally the\n",
      "     |    latest code from our repository.\n",
      "     |  - You are subscribed to the biopython-dev mailing list to provide\n",
      "     |    feedback on this code, and to be alerted of changes to it.\n",
      "     |  \n",
      "     |  If all goes well, experimental code would be promoted to stable in\n",
      "     |  a subsequent release, and this warning removed from it.\n",
      "     |  \n",
      "     |  Method resolution order:\n",
      "     |      BiopythonExperimentalWarning\n",
      "     |      BiopythonWarning\n",
      "     |      builtins.Warning\n",
      "     |      builtins.Exception\n",
      "     |      builtins.BaseException\n",
      "     |      builtins.object\n",
      "     |  \n",
      "     |  Data descriptors inherited from BiopythonWarning:\n",
      "     |  \n",
      "     |  __weakref__\n",
      "     |      list of weak references to the object (if defined)\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Methods inherited from builtins.Warning:\n",
      "     |  \n",
      "     |  __init__(self, /, *args, **kwargs)\n",
      "     |      Initialize self.  See help(type(self)) for accurate signature.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Static methods inherited from builtins.Warning:\n",
      "     |  \n",
      "     |  __new__(*args, **kwargs) from builtins.type\n",
      "     |      Create and return a new object.  See help(type) for accurate signature.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Methods inherited from builtins.BaseException:\n",
      "     |  \n",
      "     |  __delattr__(self, name, /)\n",
      "     |      Implement delattr(self, name).\n",
      "     |  \n",
      "     |  __getattribute__(self, name, /)\n",
      "     |      Return getattr(self, name).\n",
      "     |  \n",
      "     |  __reduce__(...)\n",
      "     |      Helper for pickle.\n",
      "     |  \n",
      "     |  __repr__(self, /)\n",
      "     |      Return repr(self).\n",
      "     |  \n",
      "     |  __setattr__(self, name, value, /)\n",
      "     |      Implement setattr(self, name, value).\n",
      "     |  \n",
      "     |  __setstate__(...)\n",
      "     |  \n",
      "     |  __str__(self, /)\n",
      "     |      Return str(self).\n",
      "     |  \n",
      "     |  add_note(...)\n",
      "     |      Exception.add_note(note) --\n",
      "     |      add a note to the exception\n",
      "     |  \n",
      "     |  with_traceback(...)\n",
      "     |      Exception.with_traceback(tb) --\n",
      "     |      set self.__traceback__ to tb and return self.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Data descriptors inherited from builtins.BaseException:\n",
      "     |  \n",
      "     |  __cause__\n",
      "     |      exception cause\n",
      "     |  \n",
      "     |  __context__\n",
      "     |      exception context\n",
      "     |  \n",
      "     |  __dict__\n",
      "     |  \n",
      "     |  __suppress_context__\n",
      "     |  \n",
      "     |  __traceback__\n",
      "     |  \n",
      "     |  args\n",
      "    \n",
      "    class BiopythonParserWarning(BiopythonWarning)\n",
      "     |  Biopython parser warning.\n",
      "     |  \n",
      "     |  Some in-valid data files cannot be parsed and will trigger an exception.\n",
      "     |  Where a reasonable interpretation is possible, Biopython will issue this\n",
      "     |  warning to indicate a potential problem. To silence these warnings, use:\n",
      "     |  \n",
      "     |  >>> import warnings\n",
      "     |  >>> from Bio import BiopythonParserWarning\n",
      "     |  >>> warnings.simplefilter('ignore', BiopythonParserWarning)\n",
      "     |  \n",
      "     |  Consult the warnings module documentation for more details.\n",
      "     |  \n",
      "     |  Method resolution order:\n",
      "     |      BiopythonParserWarning\n",
      "     |      BiopythonWarning\n",
      "     |      builtins.Warning\n",
      "     |      builtins.Exception\n",
      "     |      builtins.BaseException\n",
      "     |      builtins.object\n",
      "     |  \n",
      "     |  Data descriptors inherited from BiopythonWarning:\n",
      "     |  \n",
      "     |  __weakref__\n",
      "     |      list of weak references to the object (if defined)\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Methods inherited from builtins.Warning:\n",
      "     |  \n",
      "     |  __init__(self, /, *args, **kwargs)\n",
      "     |      Initialize self.  See help(type(self)) for accurate signature.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Static methods inherited from builtins.Warning:\n",
      "     |  \n",
      "     |  __new__(*args, **kwargs) from builtins.type\n",
      "     |      Create and return a new object.  See help(type) for accurate signature.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Methods inherited from builtins.BaseException:\n",
      "     |  \n",
      "     |  __delattr__(self, name, /)\n",
      "     |      Implement delattr(self, name).\n",
      "     |  \n",
      "     |  __getattribute__(self, name, /)\n",
      "     |      Return getattr(self, name).\n",
      "     |  \n",
      "     |  __reduce__(...)\n",
      "     |      Helper for pickle.\n",
      "     |  \n",
      "     |  __repr__(self, /)\n",
      "     |      Return repr(self).\n",
      "     |  \n",
      "     |  __setattr__(self, name, value, /)\n",
      "     |      Implement setattr(self, name, value).\n",
      "     |  \n",
      "     |  __setstate__(...)\n",
      "     |  \n",
      "     |  __str__(self, /)\n",
      "     |      Return str(self).\n",
      "     |  \n",
      "     |  add_note(...)\n",
      "     |      Exception.add_note(note) --\n",
      "     |      add a note to the exception\n",
      "     |  \n",
      "     |  with_traceback(...)\n",
      "     |      Exception.with_traceback(tb) --\n",
      "     |      set self.__traceback__ to tb and return self.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Data descriptors inherited from builtins.BaseException:\n",
      "     |  \n",
      "     |  __cause__\n",
      "     |      exception cause\n",
      "     |  \n",
      "     |  __context__\n",
      "     |      exception context\n",
      "     |  \n",
      "     |  __dict__\n",
      "     |  \n",
      "     |  __suppress_context__\n",
      "     |  \n",
      "     |  __traceback__\n",
      "     |  \n",
      "     |  args\n",
      "    \n",
      "    class BiopythonWarning(builtins.Warning)\n",
      "     |  Biopython warning.\n",
      "     |  \n",
      "     |  Biopython should use this warning (or subclasses of it), making it easy to\n",
      "     |  silence all our warning messages should you wish to:\n",
      "     |  \n",
      "     |  >>> import warnings\n",
      "     |  >>> from Bio import BiopythonWarning\n",
      "     |  >>> warnings.simplefilter('ignore', BiopythonWarning)\n",
      "     |  \n",
      "     |  Consult the warnings module documentation for more details.\n",
      "     |  \n",
      "     |  Method resolution order:\n",
      "     |      BiopythonWarning\n",
      "     |      builtins.Warning\n",
      "     |      builtins.Exception\n",
      "     |      builtins.BaseException\n",
      "     |      builtins.object\n",
      "     |  \n",
      "     |  Data descriptors defined here:\n",
      "     |  \n",
      "     |  __weakref__\n",
      "     |      list of weak references to the object (if defined)\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Methods inherited from builtins.Warning:\n",
      "     |  \n",
      "     |  __init__(self, /, *args, **kwargs)\n",
      "     |      Initialize self.  See help(type(self)) for accurate signature.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Static methods inherited from builtins.Warning:\n",
      "     |  \n",
      "     |  __new__(*args, **kwargs) from builtins.type\n",
      "     |      Create and return a new object.  See help(type) for accurate signature.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Methods inherited from builtins.BaseException:\n",
      "     |  \n",
      "     |  __delattr__(self, name, /)\n",
      "     |      Implement delattr(self, name).\n",
      "     |  \n",
      "     |  __getattribute__(self, name, /)\n",
      "     |      Return getattr(self, name).\n",
      "     |  \n",
      "     |  __reduce__(...)\n",
      "     |      Helper for pickle.\n",
      "     |  \n",
      "     |  __repr__(self, /)\n",
      "     |      Return repr(self).\n",
      "     |  \n",
      "     |  __setattr__(self, name, value, /)\n",
      "     |      Implement setattr(self, name, value).\n",
      "     |  \n",
      "     |  __setstate__(...)\n",
      "     |  \n",
      "     |  __str__(self, /)\n",
      "     |      Return str(self).\n",
      "     |  \n",
      "     |  add_note(...)\n",
      "     |      Exception.add_note(note) --\n",
      "     |      add a note to the exception\n",
      "     |  \n",
      "     |  with_traceback(...)\n",
      "     |      Exception.with_traceback(tb) --\n",
      "     |      set self.__traceback__ to tb and return self.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Data descriptors inherited from builtins.BaseException:\n",
      "     |  \n",
      "     |  __cause__\n",
      "     |      exception cause\n",
      "     |  \n",
      "     |  __context__\n",
      "     |      exception context\n",
      "     |  \n",
      "     |  __dict__\n",
      "     |  \n",
      "     |  __suppress_context__\n",
      "     |  \n",
      "     |  __traceback__\n",
      "     |  \n",
      "     |  args\n",
      "    \n",
      "    class MissingExternalDependencyError(builtins.Exception)\n",
      "     |  Missing an external dependency.\n",
      "     |  \n",
      "     |  Used for things like missing command line tools. Important for our unit\n",
      "     |  tests to allow skipping tests with missing external dependencies.\n",
      "     |  \n",
      "     |  Method resolution order:\n",
      "     |      MissingExternalDependencyError\n",
      "     |      builtins.Exception\n",
      "     |      builtins.BaseException\n",
      "     |      builtins.object\n",
      "     |  \n",
      "     |  Data descriptors defined here:\n",
      "     |  \n",
      "     |  __weakref__\n",
      "     |      list of weak references to the object (if defined)\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Methods inherited from builtins.Exception:\n",
      "     |  \n",
      "     |  __init__(self, /, *args, **kwargs)\n",
      "     |      Initialize self.  See help(type(self)) for accurate signature.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Static methods inherited from builtins.Exception:\n",
      "     |  \n",
      "     |  __new__(*args, **kwargs) from builtins.type\n",
      "     |      Create and return a new object.  See help(type) for accurate signature.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Methods inherited from builtins.BaseException:\n",
      "     |  \n",
      "     |  __delattr__(self, name, /)\n",
      "     |      Implement delattr(self, name).\n",
      "     |  \n",
      "     |  __getattribute__(self, name, /)\n",
      "     |      Return getattr(self, name).\n",
      "     |  \n",
      "     |  __reduce__(...)\n",
      "     |      Helper for pickle.\n",
      "     |  \n",
      "     |  __repr__(self, /)\n",
      "     |      Return repr(self).\n",
      "     |  \n",
      "     |  __setattr__(self, name, value, /)\n",
      "     |      Implement setattr(self, name, value).\n",
      "     |  \n",
      "     |  __setstate__(...)\n",
      "     |  \n",
      "     |  __str__(self, /)\n",
      "     |      Return str(self).\n",
      "     |  \n",
      "     |  add_note(...)\n",
      "     |      Exception.add_note(note) --\n",
      "     |      add a note to the exception\n",
      "     |  \n",
      "     |  with_traceback(...)\n",
      "     |      Exception.with_traceback(tb) --\n",
      "     |      set self.__traceback__ to tb and return self.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Data descriptors inherited from builtins.BaseException:\n",
      "     |  \n",
      "     |  __cause__\n",
      "     |      exception cause\n",
      "     |  \n",
      "     |  __context__\n",
      "     |      exception context\n",
      "     |  \n",
      "     |  __dict__\n",
      "     |  \n",
      "     |  __suppress_context__\n",
      "     |  \n",
      "     |  __traceback__\n",
      "     |  \n",
      "     |  args\n",
      "    \n",
      "    class MissingPythonDependencyError(MissingExternalDependencyError, builtins.ImportError)\n",
      "     |  Missing an external python dependency (subclass of ImportError).\n",
      "     |  \n",
      "     |  Used for missing Python modules (rather than just a typical ImportError).\n",
      "     |  Important for our unit tests to allow skipping tests with missing external\n",
      "     |  python dependencies, while also allowing the exception to be caught as an\n",
      "     |  ImportError.\n",
      "     |  \n",
      "     |  Method resolution order:\n",
      "     |      MissingPythonDependencyError\n",
      "     |      MissingExternalDependencyError\n",
      "     |      builtins.ImportError\n",
      "     |      builtins.Exception\n",
      "     |      builtins.BaseException\n",
      "     |      builtins.object\n",
      "     |  \n",
      "     |  Data descriptors defined here:\n",
      "     |  \n",
      "     |  __weakref__\n",
      "     |      list of weak references to the object (if defined)\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Methods inherited from builtins.ImportError:\n",
      "     |  \n",
      "     |  __init__(self, /, *args, **kwargs)\n",
      "     |      Initialize self.  See help(type(self)) for accurate signature.\n",
      "     |  \n",
      "     |  __reduce__(...)\n",
      "     |      Helper for pickle.\n",
      "     |  \n",
      "     |  __str__(self, /)\n",
      "     |      Return str(self).\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Data descriptors inherited from builtins.ImportError:\n",
      "     |  \n",
      "     |  msg\n",
      "     |      exception message\n",
      "     |  \n",
      "     |  name\n",
      "     |      module name\n",
      "     |  \n",
      "     |  path\n",
      "     |      module path\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Static methods inherited from builtins.Exception:\n",
      "     |  \n",
      "     |  __new__(*args, **kwargs) from builtins.type\n",
      "     |      Create and return a new object.  See help(type) for accurate signature.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Methods inherited from builtins.BaseException:\n",
      "     |  \n",
      "     |  __delattr__(self, name, /)\n",
      "     |      Implement delattr(self, name).\n",
      "     |  \n",
      "     |  __getattribute__(self, name, /)\n",
      "     |      Return getattr(self, name).\n",
      "     |  \n",
      "     |  __repr__(self, /)\n",
      "     |      Return repr(self).\n",
      "     |  \n",
      "     |  __setattr__(self, name, value, /)\n",
      "     |      Implement setattr(self, name, value).\n",
      "     |  \n",
      "     |  __setstate__(...)\n",
      "     |  \n",
      "     |  add_note(...)\n",
      "     |      Exception.add_note(note) --\n",
      "     |      add a note to the exception\n",
      "     |  \n",
      "     |  with_traceback(...)\n",
      "     |      Exception.with_traceback(tb) --\n",
      "     |      set self.__traceback__ to tb and return self.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Data descriptors inherited from builtins.BaseException:\n",
      "     |  \n",
      "     |  __cause__\n",
      "     |      exception cause\n",
      "     |  \n",
      "     |  __context__\n",
      "     |      exception context\n",
      "     |  \n",
      "     |  __dict__\n",
      "     |  \n",
      "     |  __suppress_context__\n",
      "     |  \n",
      "     |  __traceback__\n",
      "     |  \n",
      "     |  args\n",
      "    \n",
      "    class StreamModeError(builtins.ValueError)\n",
      "     |  Incorrect stream mode (text vs binary).\n",
      "     |  \n",
      "     |  This error should be raised when a stream (file or file-like object)\n",
      "     |  argument is in text mode while the receiving function expects binary mode,\n",
      "     |  or vice versa.\n",
      "     |  \n",
      "     |  Method resolution order:\n",
      "     |      StreamModeError\n",
      "     |      builtins.ValueError\n",
      "     |      builtins.Exception\n",
      "     |      builtins.BaseException\n",
      "     |      builtins.object\n",
      "     |  \n",
      "     |  Data descriptors defined here:\n",
      "     |  \n",
      "     |  __weakref__\n",
      "     |      list of weak references to the object (if defined)\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Methods inherited from builtins.ValueError:\n",
      "     |  \n",
      "     |  __init__(self, /, *args, **kwargs)\n",
      "     |      Initialize self.  See help(type(self)) for accurate signature.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Static methods inherited from builtins.ValueError:\n",
      "     |  \n",
      "     |  __new__(*args, **kwargs) from builtins.type\n",
      "     |      Create and return a new object.  See help(type) for accurate signature.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Methods inherited from builtins.BaseException:\n",
      "     |  \n",
      "     |  __delattr__(self, name, /)\n",
      "     |      Implement delattr(self, name).\n",
      "     |  \n",
      "     |  __getattribute__(self, name, /)\n",
      "     |      Return getattr(self, name).\n",
      "     |  \n",
      "     |  __reduce__(...)\n",
      "     |      Helper for pickle.\n",
      "     |  \n",
      "     |  __repr__(self, /)\n",
      "     |      Return repr(self).\n",
      "     |  \n",
      "     |  __setattr__(self, name, value, /)\n",
      "     |      Implement setattr(self, name, value).\n",
      "     |  \n",
      "     |  __setstate__(...)\n",
      "     |  \n",
      "     |  __str__(self, /)\n",
      "     |      Return str(self).\n",
      "     |  \n",
      "     |  add_note(...)\n",
      "     |      Exception.add_note(note) --\n",
      "     |      add a note to the exception\n",
      "     |  \n",
      "     |  with_traceback(...)\n",
      "     |      Exception.with_traceback(tb) --\n",
      "     |      set self.__traceback__ to tb and return self.\n",
      "     |  \n",
      "     |  ----------------------------------------------------------------------\n",
      "     |  Data descriptors inherited from builtins.BaseException:\n",
      "     |  \n",
      "     |  __cause__\n",
      "     |      exception cause\n",
      "     |  \n",
      "     |  __context__\n",
      "     |      exception context\n",
      "     |  \n",
      "     |  __dict__\n",
      "     |  \n",
      "     |  __suppress_context__\n",
      "     |  \n",
      "     |  __traceback__\n",
      "     |  \n",
      "     |  args\n",
      "\n",
      "VERSION\n",
      "    1.81\n",
      "\n",
      "FILE\n",
      "    c:\\users\\ijaz ali jin\\appdata\\local\\programs\\python\\python311\\lib\\site-packages\\bio\\__init__.py\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "help(Bio)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Help on package Bio.Blast in Bio:\n",
      "\n",
      "NAME\n",
      "    Bio.Blast - Code for dealing with BLAST programs and output.\n",
      "\n",
      "PACKAGE CONTENTS\n",
      "    Applications\n",
      "    NCBIWWW\n",
      "    NCBIXML\n",
      "    ParseBlastTable\n",
      "    Record\n",
      "\n",
      "FILE\n",
      "    c:\\users\\ijaz ali jin\\appdata\\local\\programs\\python\\python311\\lib\\site-packages\\bio\\blast\\__init__.py\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "help(Bio.Blast)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Help on module Bio.Blast.NCBIWWW in Bio.Blast:\n",
      "\n",
      "NAME\n",
      "    Bio.Blast.NCBIWWW - Code to invoke the NCBI BLAST server over the internet.\n",
      "\n",
      "DESCRIPTION\n",
      "    This module provides code to work with the WWW version of BLAST\n",
      "    provided by the NCBI. https://blast.ncbi.nlm.nih.gov/\n",
      "    \n",
      "    Variables:\n",
      "    \n",
      "        - email        Set the Blast email parameter (default is None).\n",
      "        - tool         Set the Blast tool parameter (default is ``biopython``).\n",
      "\n",
      "FUNCTIONS\n",
      "    qblast(program, database, sequence, url_base='https://blast.ncbi.nlm.nih.gov/Blast.cgi', auto_format=None, composition_based_statistics=None, db_genetic_code=None, endpoints=None, entrez_query='(none)', expect=10.0, filter=None, gapcosts=None, genetic_code=None, hitlist_size=50, i_thresh=None, layout=None, lcase_mask=None, matrix_name=None, nucl_penalty=None, nucl_reward=None, other_advanced=None, perc_ident=None, phi_pattern=None, query_file=None, query_believe_defline=None, query_from=None, query_to=None, searchsp_eff=None, service=None, threshold=None, ungapped_alignment=None, word_size=None, short_query=None, alignments=500, alignment_view=None, descriptions=500, entrez_links_new_window=None, expect_low=None, expect_high=None, format_entrez_query=None, format_object=None, format_type='XML', ncbi_gi=None, results_file=None, show_overview=None, megablast=None, template_type=None, template_length=None, username='blast', password=None)\n",
      "        BLAST search using NCBI's QBLAST server or a cloud service provider.\n",
      "        \n",
      "        Supports all parameters of the old qblast API for Put and Get.\n",
      "        \n",
      "        Please note that NCBI uses the new Common URL API for BLAST searches\n",
      "        on the internet (http://ncbi.github.io/blast-cloud/dev/api.html). Thus,\n",
      "        some of the parameters used by this function are not (or are no longer)\n",
      "        officially supported by NCBI. Although they are still functioning, this\n",
      "        may change in the future.\n",
      "        \n",
      "        The Common URL API (http://ncbi.github.io/blast-cloud/dev/api.html) allows\n",
      "        doing BLAST searches on cloud servers. To use this feature, please set\n",
      "        ``url_base='http://host.my.cloud.service.provider.com/cgi-bin/blast.cgi'``\n",
      "        and ``format_object='Alignment'``. For more details, please see\n",
      "        https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=CloudBlast\n",
      "        \n",
      "        Some useful parameters:\n",
      "        \n",
      "         - program        blastn, blastp, blastx, tblastn, or tblastx (lower case)\n",
      "         - database       Which database to search against (e.g. \"nr\").\n",
      "         - sequence       The sequence to search.\n",
      "         - ncbi_gi        TRUE/FALSE whether to give 'gi' identifier.\n",
      "         - descriptions   Number of descriptions to show.  Def 500.\n",
      "         - alignments     Number of alignments to show.  Def 500.\n",
      "         - expect         An expect value cutoff.  Def 10.0.\n",
      "         - matrix_name    Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).\n",
      "         - filter         \"none\" turns off filtering.  Default no filtering\n",
      "         - format_type    \"HTML\", \"Text\", \"ASN.1\", or \"XML\".  Def. \"XML\".\n",
      "         - entrez_query   Entrez query to limit Blast search\n",
      "         - hitlist_size   Number of hits to return. Default 50\n",
      "         - megablast      TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)\n",
      "         - short_query    TRUE/FALSE whether to adjust the search parameters for a\n",
      "                          short query sequence. Note that this will override\n",
      "                          manually set parameters like word size and e value. Turns\n",
      "                          off when sequence length is > 30 residues. Default: None.\n",
      "         - service        plain, psi, phi, rpsblast, megablast (lower case)\n",
      "        \n",
      "        This function does no checking of the validity of the parameters\n",
      "        and passes the values to the server as is.  More help is available at:\n",
      "        https://ncbi.github.io/blast-cloud/dev/api.html\n",
      "\n",
      "DATA\n",
      "    NCBI_BLAST_URL = 'https://blast.ncbi.nlm.nih.gov/Blast.cgi'\n",
      "    email = None\n",
      "    tool = 'biopython'\n",
      "\n",
      "FILE\n",
      "    c:\\users\\ijaz ali jin\\appdata\\local\\programs\\python\\python311\\lib\\site-packages\\bio\\blast\\ncbiwww.py\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "help(Bio.Blast.NCBIWWW)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [],
   "source": [
    "from Bio.Blast import NCBIWWW # import the NCBIWWW module from the Bio.Blast package\n",
    "\n",
    "fasta_string = open(\"seq.fasta\").read() # read the fasta file\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "result_handle = NCBIWWW.qblast(\"blastn\", \"nt\", fasta_string) # perform the blast search"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "from Bio.Blast import NCBIWWW\n",
    "from Bio.Seq import Seq\n",
    "from Bio.SeqRecord import SeqRecord\n",
    "from Bio import SeqIO\n",
    "\n",
    "# Define the input sequence\n",
    "input_seq = Seq(\"ATCGATCGATCG\")\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Create a SeqRecord object to hold the sequence and associated metadata\n",
    "seq_record = SeqRecord(input_seq, id=\"seq1\", description=\"Example sequence\")\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Write the sequence to a temporary FASTA file\n",
    "temp_fasta = \"temp.fasta\"\n",
    "SeqIO.write(seq_record, temp_fasta, \"fasta\")\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [],
   "source": [
    "import ssl\n",
    "ssl._create_default_https_context = ssl._create_unverified_context\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Run the BLAST search using the NCBIWWW.qblast() function\n",
    "result_handle = NCBIWWW.qblast(\"blastn\", \"nt\", temp_fasta)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Parse and print the results\n",
    "for blast_result in NCBIXML.parse(result_handle):\n",
    "    for alignment in blast_result.alignments:\n",
    "        for hsp in alignment.hsps:\n",
    "            print(\"****Alignment****\")\n",
    "            print(\"sequence:\", alignment.title)\n",
    "            print(\"length:\", alignment.length)\n",
    "            print(\"e value:\", hsp.expect)\n",
    "            print(hsp.query[0:75] + \"...\")\n",
    "            print(hsp.match[0:75] + \"...\")\n",
    "            print(hsp.sbjct[0:75] + \"...\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import ssl\n",
    "from Bio.Blast import NCBIWWW\n",
    "\n",
    "# Create an SSL context without certificate verification\n",
    "ssl._create_default_https_context = ssl._create_unverified_context\n",
    "\n",
    "# Read the input sequence in FASTA format\n",
    "with open(\"seq.fasta\") as f:\n",
    "    sequence = f.read()\n",
    "\n",
    "# Run BLAST and retrieve the results\n",
    "result_handle = NCBIWWW.qblast(\"blastn\", \"nt\", sequence)\n",
    "\n",
    "# Save the results to a file\n",
    "with open(\"blast_results.xml\", \"w\") as f:\n",
    "    f.write(result_handle.read())\n"
   ]
  }
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