biopython

[Sebastian Bassi]

On Mon, Jun 14, 2010 at 11:02 AM, madhuri vio <madhuri.vio at gmail.com> wrote:
> TypeError: Need a file handle, not a string (i.e. not a filename)

This says that the error is that you are using a filename where you
should be using a filehandle.
So this line:

for seq_record in SeqIO.read("ls_MTbH37Rv.fasta", "fasta"):

Should be changed to:

fh = open("ls_MTbH37Rv.fasta")
for seq_record in SeqIO.read(fh, "fasta"):

I think that in some version of Biopython you would be able to use
just the name.

Best,
SB.
Python for Bioinformatics book: http://www.tinyurl.com/biopython
Python for Bioinformatics blog: http://www.py4bio.com