[Biopython] Query
João Rodrigues
anaryin at gmail.com
Fri Jul 15 07:44:02 UTC 2011
Hello Isha,
As the error message says, you should not provide the filename to the
function, but instead a file handle. In other words, you need to open the
file first and then provide this to the function.
handle = open("ls_orchid.fasta")
> for seq_record in SeqIO.parse(handle, "fasta"):
> blablabla
Regards,
João [...] Rodrigues
http://nmr.chem.uu.nl/~joao
On Fri, Jul 15, 2011 at 9:29 AM, isha srivastava <
srivastavaisha.06 at gmail.com> wrote:
> Hello,
>
> I am new user of BioPython.
> I have Downloaded the latest version of BioPython i.e. BioPython 1.57.
> fallowed all the instructions according to tutorial.
> but wen i am running the program :
>
> >>> from Bio import SeqIO
> >>> for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
> ... print seq_record.id
> ... print repr(seq_record.seq)
> ... print len(seq_record)
> ...
>
>
> it is showing error as fallows :-
>
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/usr/lib/pymodules/python2.6/Bio/SeqIO/__init__.py", line 424, in
> parse
> raise TypeError("Need a file handle, not a string (i.e. not a
> filename)")
> TypeError: Need a file handle, not a string (i.e. not a filename)
>
> Sir, how to solve this error?
> Kindly make a soon reply.
>
>
> With due regards,
> Isha
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