BioPython遍历Fasta文件中的序列

Question

I'm new to BioPython and I'm trying to import a fasta/fastq file and iterate through each sequence, while performing some operation on each sequence. I know this seems basic, but my code below for some reason is not printing correctly.

from Bio import SeqIO

newfile = open("new.txt", "w")
records = list(SeqIO.parse("rosalind_gc.txt", "fasta"))

i = 0
dna = records[i]

while i <= len(records):
    print (dna.name)
    i = i + 1

I'm trying to basically iterate through records and print the name, however my code ends up only printing "records[0]", where I want it to print "records[1-10]". Can someone explain why it ends up only print "records[0]"?

Answer 1

The reason for your problem is here:

i = 0
dna = records[i]

Your object 'dna' is fixed to the index 0 of records, ie, records[0]. Since you are not calling it again, dna will always be fixed on that declaration. On your print statement within your while loop, use something like this:

while i <= len(records):
    print (records[i].name)
    i = i + 1

If you would like to have an object dna as a copy of records entries, you would need to reassign dna to every single index, making this within your while loop, like this:

while i <= len(records):
    dna = records[i]
    print (dna.name)
    i = i + 1

However, that's not the most efficient way. Finally, for you to learn, a much nicer way than with your while loop with i = i + 1 is to use a for loop, like this:

for i in range(0,len(records)):
    print (records[i].name)

For loops do the iteration automatically, one by one. range() will give a set of integers from 0 to the length of records. There are also other ways, but I'm keeping it simple.