## do not remove the extra print statements
print('Question 1')
#################################################################
# QUESTION 1                                                    #
#   
# In lecture, we saw how to write code to read a genome FASTA file. 
# The autograder will contain a genome fasta file in the path provided 
# below.
#
# As with most FASTA files, there will be two types of lines. 
# One has the ">" sign and is the definition line (define) of each 
# chromosome. The other lines constitute genomic sequences.
#
# Write a script to read through the file to collect deflines and
# remove the ">" sign before those deflines. You should also 
# define a new list before you read the file.
#
# Your code should append each defline to the list if the length
# of the defline is less than 3 after the ">" is removed.
#
# Then, after reading through the file, use the join() method 
# to join all deflines in the list into a string, using the comma
#  (,) character as a separator.
#
# Last, print the string you created, which should be a comma-
# separated collection of chromosome names on just one line of text.
#
#################################################################


genome_fasta = '/autograder/source/dm6.fa'
##add code for question 1 here



## do not remove the extra print statements
print('Question 2')
#################################################################
# QUESTION 2                                                    #
#                                                               #
# First, for the list of DNA sequences below, combine them into
# one sequence by concatenation (hint: you should be able to do 
# that in one step). Print out the sequence on one line.
#
# Second, calculate the GC-content for the concatenated sequence
# you just print and print the GC-content as a percentage with 
# two decimal places (not two sig figs, just two digits after the 
# decimal/dot (.). Print this out one one line just as a number,
# no extra headers and no percent symbol.
# This answer should have two lines of text. 
#
#################################################################

DNA = ['GCTGATCGTACTACG','GCTACGTACTACTAC','GCGCGTACGCTAC','GCATCTGACGCGCGTAACG']
##add code for question 2 here


## do not remove the extra print statements
print('Question 3')
#################################################################
# QUESTION 3                                                    #
#                                                               #
# Given the following string, write code that will do the 
# following tasks:
# 
# 1. split the string on the newline character ('\n') and assign
#  the resulting elements to a list.
#
# 2. join the elements of the list together using join() and using 
# the empty string as a delimiter.
#
# 3. print out the resulting string as one line of text.
#
#################################################################

sequences = "ATCGTAGCT\nAATCAGCTCGCTA\nTCTCAGAGATT"
##add code for question 3 here



## do not remove the extra print statements
print('Question 4')
#################################################################
# QUESTION 4                                                    #
#                                                               #
# For the genome fasta mentioned above in Question 1, Write some 
# code to read through the file, and store the genomic 
# sequences into a dictionary of lists with the chromosome name 
# as the key and a list of strings as the value. Next use the 
# join method to create a dictionary of strings, also with the 
# chromosome name as the key, but the full genome sequence as 
# the value. This was basically done in an exploration page. 
# Lastly, print the length of chromosome "2L".
# Your answer below should just be length of chromosme 2L, a number
# on line line.
#
#################################################################


genome_fasta = '/autograder/source/dm6.fa'
##add code for question 4 here



## do not remove the extra print statements
print('Question 5')
#####################################################################
# QUESTION 5                                                        #
#                                                                   #
# There is a bed file with the autograder in the path defined below
# please read in the bed file using the methods described in class.
# Store the columns of the file as a list of tuples. You must only 
# store the chromosom, start, and end positions (columns 1,2, and 3)
# in that order. 
# and store the start and end as int data types, and the chromosome name 
# as a string. Then print out the list of tuples just a as list like:
# print(L) which should output it on line line (as opposed to looping 
# through the tuples and printing out each tuple, which you should not 
# do here)
#####################################################################


bed_file = '/autograder/source/example.bed'
##add code for question 5 here