Created
July 16, 2010 05:27
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""" | |
%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") |
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.
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hi,
where is the file being taken as input?
thanks