It sounds like all you really want is to print every 2nd line of a text file. If so, you don't need Python, let alone BioPython, you can do it with basic *nix tools:
$ awk 'NR%4==2' pdb.fasta_qual.dataset
247
NR is the current line number, and % is the modulo operator. Therefore, NR % 4 will equal 2 on the second line of each group of 4 lines in the file. In awk, the default action when something evaluates to true is to print the current line, so this will print out all length lines from your input file (assuming you don't have blank lines anywhere, which we don't know since you only showed the first entry).
If you want to add some sort of message to be printed, you could do:
$ awk 'NR%4==2{ print "The length of protein",++c,"is:",$0}' pdb.fasta_qual.dataset
The length of protein 1 is: 247
If you really must do this in Python, you could do something like this:
#!/usr/bin/env python3
import sys
#my_file= sys.argv[1]
line_number = 0
with open(sys.argv[1]) as f:
for line in f:
line_number += 1
if (line_number % 4 == 2):
print("The length of protein %d is: %d" % (line_number,int(line.strip())))
And then you would run it like this (assuming you named the script foo.py):
$ python3 foo.py pdb.fasta_qual.dataset
The length of protein 2 is: 247
Out of curiosity, I created a test file by repeating your example 10000000 times, which left me with a 2.4G file:
$ perl -e 'open(A,"pdb.fasta_qual.dataset"); @lines=<A>; print "@lines" x 10000000' > testFile
$ ls -lh testFile
-rw-r--r-- 1 terdon terdon 2.4G Feb 7 17:06 testFile
I then tested both approaches for speed. Unsurprisingly, awk was much faster:
$ time awk 'NR%4==2' testFile > /dev/null
real 0m6.447s
user 0m5.917s
sys 0m0.492s
$ time foo.py testFile > /dev/null
real 0m10.856s
user 0m10.111s
sys 0m0.523s