old_contents: #!/usr/bin/python
  import sqlite3
  
  
  # THIS file will parse in two files named 'DRdatabase' and 'Spacerdatabase',
  # and populate the 'crispr.sqlite' file tables Spacers and Repeats, as per 
  # ISSUE #99 https://github.com/goyalsid/phageParser/issues/99
  
  def read_input_file(filename):
      fin = open(filename, 'r')
      flines = fin.readlines()
      file_dict = dict()
      for f in flines:
          f = f.replace('\n', '')
          if f[0] == '>':
              accessions = f[1:].split('|')
          else:
              file_dict[f] = accessions
      return file_dict
  
  
  def print_dict(d):
      for i in d:
          print(i, d[i])
  
  
  def get_largest_id(c, name, id_name):
      # NOT USED
      # SELECT * FROM Spacer ORDER BY SpacerID DESC LIMIT 1
      q = "SELECT * FROM " + name + " ORDER BY " + id_name + " DESC LIMIT 1"
      c.execute(q)
      return c.fetchone()[0]
  
  
  def sql_add(elem, name, db_name):
      conn = sqlite3.connect(db_name)
      c = conn.cursor()
      col_name = name + 'Sequence'
      q = "INSERT INTO " + str(name) + " (" + str(
          col_name) + ") VALUES ('" + elem + "')"
      try:
          c.execute(q)
          conn.commit()
      except sqlite3.IntegrityError:
          print("Already In Database", elem)
      c.close()
      conn.close()
  
  
  def sql_search(elem, name, column, db_name):
      conn = sqlite3.connect(db_name)
      c = conn.cursor()
      q = "SELECT * FROM " + name + "  WHERE " + column + " = '" + elem + "'"
      # print q
      c.execute(q)
      r = c.fetchone()
      c.close()
      conn.close()
      return r
  
  
  def populate_db(db_name, table_name, file_name):
      input_dict = read_input_file(file_name)
      for d in input_dict:
          sql_add(d, table_name, db_name)
  
  
  repeat_file = 'data/DRdatabase.txt'
  spacer_file = 'data/spacerdatabase.txt'
  db_name = 'crispr.sqlite'
  
  populate_db(db_name, 'Repeat', repeat_file)
  populate_db(db_name, 'Spacer', spacer_file)
  
new_contents: #!/usr/bin/python
  import sqlite3
  
  
  # THIS file will parse in two files named 'DRdatabase' and 'Spacerdatabase',
  # and populate the 'crispr.sqlite' file tables Spacers and Repeats, as per 
  # ISSUE #99 https://github.com/goyalsid/phageParser/issues/99
  
  def read_input_file(filename):
      fin = open(filename, 'r')
      flines = fin.readlines()
      file_dict = dict()
      for f in flines:
          f = f.replace('\n', '')
          if f[0] == '>':
              accessions = f[1:].split('|')
          else:
              file_dict[f] = accessions
      return file_dict
  
  
  def print_dict(d):
      for i in d:
          print(i, d[i])
  
  
  def get_largest_id(c, name, id_name):
      # NOT USED
      # SELECT * FROM Spacer ORDER BY SpacerID DESC LIMIT 1
      q = "SELECT * FROM " + name + " ORDER BY " + id_name + " DESC LIMIT 1"
      c.execute(q)
      return c.fetchone()[0]
  
  
  def sql_add(elem, name, db_name):
      conn = sqlite3.connect(db_name)
      c = conn.cursor()
      col_name = name + 'Sequence'
      q = ("INSERT INTO " + str(name) + " (" + str(col_name)
           + ") VALUES ('" + elem + "')")
      try:
          c.execute(q)
          conn.commit()
      except sqlite3.IntegrityError:
          print("Already In Database", elem)
      c.close()
      conn.close()
  
  
  def sql_search(elem, name, column, db_name):
      conn = sqlite3.connect(db_name)
      c = conn.cursor()
      q = "SELECT * FROM " + name + "  WHERE " + column + " = '" + elem + "'"
      # print q
      c.execute(q)
      r = c.fetchone()
      c.close()
      conn.close()
      return r
  
  
  def populate_db(db_name, table_name, file_name):
      input_dict = read_input_file(file_name)
      for d in input_dict:
          sql_add(d, table_name, db_name)
  
  
  repeat_file = 'data/DRdatabase.txt'
  spacer_file = 'data/spacerdatabase.txt'
  db_name = 'crispr.sqlite'
  
  populate_db(db_name, 'Repeat', repeat_file)
  populate_db(db_name, 'Spacer', spacer_file)
  
subject: Add parentheses to fix odd formatting