Extract data - pickled version.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "26fe1b52-93c0-4af9-9830-9f170f9bad0b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Requirement already satisfied: forgi in /Users/Study/opt/anaconda3/lib/python3.9/site-packages (2.1.2)\n",
      "Requirement already satisfied: pandas>=0.20 in /Users/Study/opt/anaconda3/lib/python3.9/site-packages (from forgi) (1.4.4)\n",
      "Requirement already satisfied: future in /Users/Study/opt/anaconda3/lib/python3.9/site-packages (from forgi) (0.18.2)\n",
      "Requirement already satisfied: logging-exceptions>=0.1.8 in /Users/Study/opt/anaconda3/lib/python3.9/site-packages (from forgi) (0.1.8)\n",
      "Requirement already satisfied: numpy>=1.10.0 in /Users/Study/opt/anaconda3/lib/python3.9/site-packages (from forgi) (1.21.5)\n",
      "Requirement already satisfied: cython in /Users/Study/opt/anaconda3/lib/python3.9/site-packages (from forgi) (0.29.32)\n",
      "Requirement already satisfied: biopython in /Users/Study/opt/anaconda3/lib/python3.9/site-packages (from forgi) (1.81)\n",
      "Requirement already satisfied: scipy>=0.19.1 in /Users/Study/opt/anaconda3/lib/python3.9/site-packages (from forgi) (1.9.1)\n",
      "Requirement already satisfied: appdirs>=1.4 in /Users/Study/opt/anaconda3/lib/python3.9/site-packages (from forgi) (1.4.4)\n",
      "Requirement already satisfied: networkx>=2.0 in /Users/Study/opt/anaconda3/lib/python3.9/site-packages (from forgi) (2.8.4)\n",
      "Requirement already satisfied: python-dateutil>=2.8.1 in /Users/Study/opt/anaconda3/lib/python3.9/site-packages (from pandas>=0.20->forgi) (2.8.2)\n",
      "Requirement already satisfied: pytz>=2020.1 in /Users/Study/opt/anaconda3/lib/python3.9/site-packages (from pandas>=0.20->forgi) (2022.1)\n",
      "Requirement already satisfied: six>=1.5 in /Users/Study/opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas>=0.20->forgi) (1.16.0)\n"
     ]
    }
   ],
   "source": [
    "!pip install forgi"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "a681259e-51b3-4ccb-b6bb-556968afbeb6",
   "metadata": {},
   "outputs": [],
   "source": [
    "import forgi \n",
    "import forgi.graph.bulge_graph as fgb\n",
    "import os\n",
    "import shutil \n",
    "import pickle "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "10d2a125-3bed-4eba-ac76-082496f900ba",
   "metadata": {},
   "outputs": [],
   "source": [
    "def main(DBN_folder_path,dest_path,min_length):\n",
    "  '''\n",
    "  :DBN_folder_path: the path of the parent file of all DBN target files\n",
    "                    target DBN files include free energy value\n",
    "                    note that the parent folder should include DBN files only\n",
    "                    the programm can only filter out .DS_S files but not any other file types\n",
    "                    \n",
    "  :dest_path: the path of the parent file of the file that will include all new DBN files\n",
    "                    new DBN files don't include free enrgy value, know as FASTA accoridng to the forgi documentation \n",
    "                    \n",
    "  '''\n",
    "\n",
    "  #dest_path is the path of the parent folder of the new folder \n",
    "  new_DBN_folder_path=copyFolder(DBN_folder_path,dest_path,'_DBNfiles')\n",
    "\n",
    "\n",
    "  #create folder that will contain all pickled files\n",
    "  new_folder_name= os.path.basename(DBN_folder_path)+'_pickled'\n",
    "  data_dir=os.path.join(dest_path,new_folder_name)\n",
    "  os.mkdir(data_dir)\n",
    "\n",
    "  ##iterate over new DBN files in order to modify them to *regular* DBN files \n",
    "  abs_paths_DBN_files= absoluteFilePaths(new_DBN_folder_path)\n",
    "\n",
    "  i=0\n",
    "  for DBN_file_path in abs_paths_DBN_files:\n",
    "    contig_name = os.path.basename(DBN_file_path)[:-4]\n",
    "    if contig_name == '.DS_S' or ContigIsSmall(DBN_file_path,min_length):\n",
    "        print(contig_name,'skipped')\n",
    "        continue \n",
    "    i+=1\n",
    "    print(i,'working on ',contig_name)\n",
    "    free_energy=getFreeEnergy(DBN_file_path) #changes DBN file\n",
    "    contig=Contig(DBN_file_path,free_energy)\n",
    "    pickle_path=os.path.join(data_dir,contig_name)\n",
    "    with open(pickle_path, 'wb') as handle:\n",
    "       pickle.dump(contig, handle, protocol=pickle.HIGHEST_PROTOCOL)\n",
    "\n",
    "\n",
    "\n",
    "  return "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "97ed8ea9-fbc6-4dae-a2fa-f80b39de286d",
   "metadata": {},
   "outputs": [],
   "source": [
    "class Contig:\n",
    "  def __init__(self,DBN_file_path,free_energy):\n",
    "    self.bg, =fgb.BulgeGraph.from_fasta(DBN_file_path)\n",
    "    self.name = os.path.basename(DBN_file_path)[:-4]\n",
    "    self.length= self.bg.seq_length\n",
    "    self.free_energy = float(free_energy)\n",
    "    self.unpaired_ratio=100*(countUnpaired(DBN_file_path)/(self.length))\n",
    "    self.stems=Contig.countStems(self.bg)\n",
    "    self.hairpins=Contig.countHairpins(self.bg)\n",
    "    self.interior_loops= Contig.countInteriorLoops(self.bg)\n",
    "    self.multiloops= Contig.countMultiloops(self.bg)\n",
    "\n",
    "\n",
    "  def countStems(bg):\n",
    "    cnt=0\n",
    "    for h in bg.stem_iterator():\n",
    "      cnt+=1\n",
    "    return cnt\n",
    "\n",
    "\n",
    "  def countHairpins(bg):\n",
    "    cnt=0\n",
    "    for h in bg.hloop_iterator():\n",
    "      cnt+=1\n",
    "    return cnt\n",
    "\n",
    "  def countInteriorLoops(bg):\n",
    "    cnt=0\n",
    "    for i in bg.iloop_iterator():\n",
    "      cnt+=1\n",
    "    return cnt\n",
    "\n",
    "  def countMultiloops(bg):\n",
    "    junctions=bg.junctions\n",
    "    reg_multiloops=[]\n",
    "    cnt=0\n",
    "    for el in junctions:\n",
    "      if bg.describe_multiloop(el)=={'regular_multiloop'}:\n",
    "        cnt +=1\n",
    "    return cnt \n",
    "\n",
    "\n",
    "  def describe_contig(self):\n",
    "    print('name = ',self.name)\n",
    "    print('length = ',self.length)\n",
    "    print('free_energy = ',self.free_energy )\n",
    "    print('unpaired = ',self.unpaired_ratio)\n",
    "    print('stems = ',self.stems)\n",
    "    print('hairpins = ',self.hairpins)\n",
    "    print('interior_loops = ',self.interior_loops)\n",
    "    print('multiloops = ',self.multiloops)\n",
    "\n",
    " "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "4fda4ce4-06f2-4d0f-8592-b014d750738d",
   "metadata": {},
   "outputs": [],
   "source": [
    "def ContigIsSmall(DBN_file_path,min_length):\n",
    "    with open(DBN_file_path, 'r') as dbn:\n",
    "        lines = dbn.readlines()\n",
    "        length= len(lines[1].strip())\n",
    "    return (length<min_length)\n",
    "\n",
    "\n",
    "def copyFolder(original_folder_path,destination,suffix):\n",
    "  new_folder_name= os.path.basename(original_folder_path)+suffix\n",
    "  new_folder_path=os.path.join(destination,new_folder_name)\n",
    "  shutil.copytree(original_folder_path, new_folder_path)\n",
    "  return new_folder_path\n",
    "\n",
    "def absoluteFilePaths(directory):\n",
    "  for dirpath,_,filenames in os.walk(directory):\n",
    "      for f in filenames:\n",
    "          yield os.path.abspath(os.path.join(dirpath, f))\n",
    "\n",
    "#returns free energy and !!!updates!!! DBN file to regular DBN file by removing free energy - value from line 2\n",
    "def getFreeEnergy(DBN_file_path):\n",
    "  with open(DBN_file_path,'r') as file:\n",
    "    content = file.readlines()\n",
    "  DBNstr = \"\"\n",
    "  FreeEnergy = \"\"\n",
    "  i=-1\n",
    "  for x in content[2]:\n",
    "    i +=1\n",
    "    if x != \" \":\n",
    "      DBNstr+=x\n",
    "    else:\n",
    "      break\n",
    "  for j in range(i+2,len(content[2])-2):\n",
    "    FreeEnergy += content[2][j]\n",
    "  content[2]=DBNstr\n",
    "  with open(DBN_file_path,'w') as file:\n",
    "    file.writelines(content)\n",
    "  return FreeEnergy \n",
    "\n",
    "def countUnpaired(DBN_file_path):\n",
    "  with open(DBN_file_path,'r') as file:\n",
    "    content = file.readlines()\n",
    "  cnt=0\n",
    "  for ch in content[2]:\n",
    "    if (ch =='.'):\n",
    "      cnt+=1\n",
    "  return cnt \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "b31218f9-dbfa-4ce3-b56f-752f52902107",
   "metadata": {},
   "outputs": [
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     ]
    }
   ],
   "source": [
    "main('/Users/Study/Desktop/BIO project/Data/DBN files/levi','/Users/Study/Desktop/BIO project/Data/Pickled/leviviridae',min_length=3000)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d837eeac-d787-4d34-b114-3aa19fcd9fbc",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8a4d926f-f1e0-44b0-b1db-de5f817ac795",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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