Question

1. Counting Severe Acute Respiratory Syndrome coronavirus 2 genome bps: Download the FASTA file (NC_045512.2) containing the SARS-CoV-2 reference sequence. (You can use the "Send" widget on the upper-right corner of the NCBI Web page containing the genome to download a FASTA file.) Now, write a Python program that reads the file, stores the sequence without white characters (spaces, end-of-line, etc.), and prints out the number of nucleotides (bps) in the complete SARS-CoV-2 genome.

Answer 1

Here is the code:

f = open ("NC_045512.2.fna")
f.readline() # Ignore the header
c = f.readlines ()

l = ""
for e in c:
l += e.strip()

print (len(l))
#--- E N D O F C O D E

29903                                                                                                                         

                                                                                                                              

                                                                                                                              

...Program finished with exit code 0

The NCBI site also shows 29903 as the number of bps, confirming above answer:

Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome

Severe acute respiratory syndrome coronavirus 2

29,903 bp genomic sequence

• NC_045512.2