gistfile1.py

"""                                                                                 
%prog some.fasta wanted-list.txt                                                    
"""                                                                                 
from Bio import SeqIO                                                               
import sys                                                                          
                                                                                    
wanted = [line.strip() for line in open(sys.argv[2])]                               
seqiter = SeqIO.parse(open(sys.argv[1]), 'fasta')                                    
SeqIO.write((seq for seq in seqiter if seq.id in wanted), sys.stdout, "fasta")

hi,
where is the file being taken as input?
thanks

It takes two input files. The initial comment line addresses that question:
%prog some.fasta wanted-list.txt

For example when I ran this, I typed:
python gistfile1.py my_big_file.fasta just_the_names_I_need.txt

Also, I changed sys.stdout in line 9 to 'output.txt' so it would save to file rather than printing to screen.

I tried changing the sys.stout to an output file name with no luck instead receiving the error that the file name was undefined, is there any possible way to fix this?
Yet if I leave as sys.stdout I am not receiving an output.