Please help me with this. Write a Python program (version 3.5) that analyzes DNA

Question

Please help me with this. Write a Python program (version 3.5) that analyzes DNA sequences (or strings). A DNA string consists of the alphabet A (adenine), C (cytosine), G (guanine), and T (thymine).

Your program will ask the user for the name of a DNA sequence file in FASTA format, which is a text-based format for representing DNA sequences. Then, it will print a report on the entire set of sequences consisting of:

• the number of sequences in the input file,

• the total length of all sequences,
• the maximum sequence length,
• the minimum sequence length, and

• the average length of the sequences.

For each sequence, print:

• the header line,
• the length of the sequence, and
• the number of nucleotides A, C, G, and T in the sequence.

I uploaded the txt files you need to use to dropbox on this link:

https://www.dropbox.com/sh/cgp3zun785z6o11/AAD0Y7vknEhTh8Bth7D_MBoma?dl=0

Please post a screenshot of the code so that I see the indentation.

Explanation / Answer

# -*- coding: utf-8 -*- """ The program includes a set of tools for dna sequence analyses. To use the tool sets, please assign the path and file name to the class function. For example: dna_tools = dna_tool_sets ("../data/dna.example.fasta") Then, call the functions in the class, e.g call function to check length of dna sequence: length = dna_tools.check_length() """ class dna_tool_sets (): """ This class includes a set of tools for dna sequence analyses: a. count_records b. check_length c. orf_identifier d. repeats_identifier parameter: file name including path directory Note: the file should be in FASTA format """ def __init__(self, file_name): """ this function open input file and transform each record to dictornary the key and value of the dict are header and dna sequence of the record, respectively """ self.file_name = file_name # initiate loading file self.dict = {} # initiate an empty dictornary f_reader = open (self.file_name) for line in f_reader: line = line.strip(" ") # remove " " in line if ">" in line: # check if this line is a header header = line # assign line to header self.dict[header] = "" #add header to dictornary with an initial empty string else: self.dict[header] += line # add dna sequence to the header accordingly f_reader.close() def count_records (self): """ this function count number of records in the file""" number_of_records = len(self.dict) # check records in dictornary # Q1: How many records are in the multi-FASTA file? print "Q1: How many records are in the multi-FASTA file: %d " %number_of_records #return number_of_records def check_length(self): """ this function check length of each record and the according header of the record """ length_dict = {} # creat a dictornary to record length of each record for key, value in self.dict.items(): length_dict[key] = len(value) lengths = length_dict.values() # count length for each sequence max_length = max(lengths) # max length of sequences min_length = min(lengths) # min length of sequences # identifier of sequences with max length record_max_length = [item for item in length_dict if length_dict[item] == max_length] # identifier of sequences with min length record_min_length = [item for item in length_dict if length_dict[item] == min_length] # Q2: What is the length of the longest sequence in the file? print "Q2: The length of the longest sequence: %d "%max_length, "The number of longest sequence: %d "%len(record_max_length) # Q3: What is the length of the shortest sequence in the file? print "Q3: The length of the shortest sequence: %d "%min_length, "The number of shortest sequence: %d "%len(record_min_length) # uncomment the return code to return the whole length information for # each record #return length_dict def find_pos(self, dna): """ help function for orf_identifier: find start position and length for each read frame for a given sequence dna: sequence, string """ start_code = "ATG" stop_codes = ["TAA", "TAG", "TGA"] pos_dict = {} #record orfs of each frame to dictornary for i in range(3): # walk through 3 different frames # record strat position and length for each frame to a list pos = [] # generate frames if i == 0: frame = [dna[j:j+3] for j in range(i, len(dna), 3)] else: frame = [dna[:i]] + [dna[j:j+3] for j in range(i, len(dna), 3)] # find all possible start postions and stop positions start_pos = [] stop_pos = [] try: index_start_pos = [m for m, y in enumerate(frame) if y == start_code] start_pos += index_start_pos # find possible positions for start code "ATG" except ValueError: pos.append((-1, 0)) # return -1 as start position if no ATG continue for stop_code in stop_codes: try: # find all possible positions of stop codes index_stop_code = [n for n, x in enumerate(frame) if x == stop_code and n > min(start_pos)] stop_pos += index_stop_code except ValueError: continue if len(stop_pos) == 0: # add -1 as start position when no stop code find pos.append((-1, 0)) else: #find the closest paired code while len(start_pos) != 0: start = min(start_pos) try: end = min([stop for stop in stop_pos if stop > start]) except ValueError: break # add start position and length s_pos = len("".join(frame[:start])) + 1 pos.append((s_pos, (end - start + 1)*3)) start_pos.remove(start) pos_dict["frame%d"%(i+1)] = pos return pos_dict def revs_complement(dna): """ help function for orf_identifier: to transform a sequence to reverse complementary sequence """ pairs = {"A": "T", "C": "G", "G": "C", "T": "A"} # complementary code c_dna = [pairs[s] for s in dna] # complementary replace return "".join(c_dna)[::-1] # reverse def orf_identifier (self): """ This function return all the orf information with start posiotion and length of orf in read frame 1, 2 and 3 the values for frame 1, 2, and are represented as pairs of tuple in a list for example: {"header1": {"frame1":[(0, 100)], "frame2":[(20, 400)], "frame3":[(-1, 0)]},...} represents for header1: frame1- start position: 0, length of orf: 100 frame2- start position: 20, length of orf: 400 frame3- No ORF detected """ orf = {} for header, dna_seq in self.dict.items(): # generate orf for the whole file pos = self.find_pos(dna_seq) orf[header] = pos # find header for question 7 id_key = [key for key in orf if "gi|142022655|gb|EQ086233.1|129" in key] idx = id_key[0] # generate list of frames for questions 4 to 7 frame1, frame2, all_frames, id_frames = [], [], [], [] for key, dict_value in orf.items(): frame1 += dict_value["frame1"] frame2 += dict_value["frame2"] frames = dict_value["frame1"] + dict_value["frame2"] + dict_value["frame3"] all_frames += frames if key == idx: id_frames = dict_value["frame1"] + dict_value["frame2"] + dict_value["frame3"] #Q4: What is the length of the longest ORF appearing in reading #frame 2 of any of the sequences? frame2_max_length = max(frame2, key = lambda x: x[1]) print "Q4: The length of longest ORF in frame2: %d "%frame2_max_length[1] #Q5: What is the starting position of the longest ORF in reading frame 1 #in any of the sequences? frame1_max_length_pos = max(frame1, key = lambda x: x[1]) print "Q5: The start position of longest ORF in frame1: %d "%frame1_max_length_pos[0] #Q6: What is the length of the longest ORF appearing in any sequence and #in any forward reading frame? max_length = max(all_frames, key = lambda x: x[1]) print "Q6: The longest ORF of all frames and sequences: %d "%max_length[1] #Q7: What is the length of the longest forward ORF that appears in the #sequence with the identifier gi|142022655|gb|EQ086233.1|129? max_length_id = max(id_frames, key = lambda x: x[1]) print "Q7: The length of longest ORF for ", idx, "is: %d " %max_length_id[1] # uncomment the return code to return the whole orf information #including starting position and length of each frame for each sequence #return orf def find_repeats(self, dna, n): """ This help function for repeats_identifier find and count repeats for each dna sequence dna: sequence, string n: number of repeats, int """ repeats = {} for i in range(0, len(dna)): repeat = dna[i:i+n] # generate possible repeats if len(repeat) == n: if repeat not in repeats: repeats [repeat] = 1 # initiate record else: # count repeated repeats repeats[repeat] = repeats.get(repeat) + 1 return repeats def repeats_identifier(self, n): """ This function generates repeats with counts for each record (repeats_set) and for the whole file (combined_repeats) n: number of repeats, int """ # record the repeats with counts for each record repeats_set = {} for header, dna_seq in self.dict.items(): repeats = self.find_repeats(dna_seq, n) repeats_set[header] = repeats # record the repeats with counts for the whole file combined_repeats = {} for dict_value in repeats_set.values(): for key in dict_value: if key not in combined_repeats: combined_repeats[key] = dict_value[key] else: combined_repeats[key] = combined_repeats.get(key) + dict_value[key] # Q8:Find the most frequently occurring repeat of length 7 in all # sequences. How many times does it occur in all? if n == 7: most_freq_7 = max (combined_repeats.values()) print "Q8: The most frequently repeats occur: %d times "%most_freq_7 # Q10:Which one of the following repeats of length 7 has a maximum #number of occurrences? most_freq_7_seq = [key for key in combined_repeats if combined_repeats[key] == max(combined_repeats.values())] print "Q10: The following repeats occured most frequently: ", most_freq_7_seq # Q9:Find all repeats of length 10 in the input file. Let's use Max to #specify the number of copies of the most frequent repeat of length 10. #How many different 10-base sequences occur Max times? if n == 10: # answer question 9 count_most_freq_10 = len([value for value in combined_repeats.values() if value == max(combined_repeats.values())]) print "Q9: The number of different 10-base sequences occur max times: %d " %count_most_freq_10 # uncomment the return code to return the repeats with counts for each record # (repeats_set) and for the whole file (combined_repeats) #return repeats_set, combined_repeats if __name__ == "__main__": file_name = "../data/dna3.fasta" dna_tools = dna_tool_sets (file_name) # Q1: How many records are in the multi-FASTA file? dna_tools.count_records() # Q2: What is the length of the longest sequence in the file? # Q3: What is the length of the shortest sequence in the file? dna_tools.check_length() #Q4: What is the length of the longest ORF appearing in reading #frame 2 of any of the sequences? #Q5: What is the starting position of the longest ORF in reading frame 1 #in any of the sequences? #Q6: What is the length of the longest ORF appearing in any sequence and #in any forward reading frame? #Q7: What is the length of the longest forward ORF that appears in the #sequence with the identifier gi|142022655|gb|EQ086233.1|129? dna_tools.orf_identifier() # Q8:Find the most frequently occurring repeat of length 7 in all # sequences. How many times does it occur in all? # Q10:Which one of the following repeats of length 7 has a maximum #number of occurrences? dna_tools.repeats_identifier(7) # Q9:Find all repeats of length 10 in the input file. Let's use Max to #specify the number of copies of the most frequent repeat of length 10. #How many different 10-base sequences occur Max times? dna_tools.repeats_identifier(10)

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