Question

I need to create a Bed module with these functions:

readBed(file)
–
read 
a 
BED 
format 
file 
and
 constructs 
a 
list 
of 
gene 
model 
objects 
from 
the
 data
 it 
contains.



writeBed(models=models,fname=file)
 – 
writes 
the 
given 
list
 of
 gene 
model 
objects
 and 
 writes
 them 
to 
a
 file 
named 
fname.

For the readBed, I was thinking about readline function that I have wrote before, and add the codes for it to return a result as a list. For writeBed, I really am clueless. Here is my codes, please guide me everyone:

def ReadBed(file):
  result = []
  line = fh.readline()
  if not line:
      fh.close()
  else:
      return result

def writeBed(models=models, fname=file):
  if file.ReadBed = result
  return result in fname

Also, I had a Range class like this, and I want to raise TypeError and ValueError for my class, but not sure how to do it, can everyone please help me too. Thank you so much everyone:

class Range:
  def __init__(self, start, end):
    self.setStart(start)
    self.setEnd(end)
  def getStart(self):
    return self.start
  def setStart(self, s):
    self.start = s
  def getEnd(self):
    return self.end
  def setEnd(self, e):
    self.end = e
  def getLength(self):
    return len(range(self.start, self.end))
  def overlaps(self, r):
    if (r.getStart() < self.getEnd() and r.getEnd() >= self.getEnd()) or \
       (self.getStart() < r.getEnd() and self.getEnd() >= r.getEnd()) or \
       (self.getStart() >= r.getStart() and self.getEnd() <= r.getEnd()) or \
       (r.getStart() >= self.getStart() and r.getEnd() <= self.getEnd()):
      return True
    else:
      return False

Answer 1

Without knowing the format in which the data is saved to file, I can only assume that it is being pickled. With that assumption in mind, I can give you the following code:

import cPickle

def readBed(filepath):
    with open(filepath, 'r') as f:
        data = cPickle.load(f)
        return data

def writeBed(models, filepath):
    with open(filepath, 'w') as f:
        cPickle.dump(models, f)