Download the complete genome sequence (..genomic.fna) for the bacterium Clostrid

Question

Download the complete genome sequence (..genomic.fna) for the bacterium Clostridium phytofermentans from ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Lachnoclostridium_phytofermentans/representative/GCF_000018685.1_ASM1868v1/ (or your favorite bacterial genome sequence). Write a program that inputs this sequence (discard the first line with the > fasta header) and writes to an output file a tab formatted file (Hint: use and in your .write statement) with the nucleotide counts and the total number of nucleotides.

Explanation / Answer

def readfile(filename):

                nucleotides_dict = {}

                with open(filename,'r') as f:        #opens file in read mode

                                next(f) #skips first line

                                lines = f.readlines()         #reads file data into list

                                try:

                                                data = ''.join(lines)           #convert list into string

                                                data = data.replace(' ','')            #replace newline characters

                                                total_nucleotides = len(data)     #total characters ib string

                                                nucleotides = list(set(data))        #unique characters in string

                                                for nucleotide in nucleotides:     #counts count of nucleotide

                                                                nucleotides_dict.update({nucleotide:data.count(nucleotide)})

                                                nucleotides_dict.update({'Total':total_nucleotides})

                                except Exception as e:

                                                print (e)

                return nucleotides_dict

def writefile(nucleo_dict):

                with open('output.txt','w') as f: #open file in write mode

                                for key,value in nucleo_dict.items():

                                                line = key+' '+str(value)+' '

                                                f.write(line)

if __name__ == '__main__':

                filepath = ''                                                                                          #full path to GCF_000018685.1_ASM1868v1_genomic.fna

                nucleo_dict = readfile(filepath)                 #reads file

                writefile(nucleo_dict)                                                    #write data to file

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