Re: biopython

[Mark Lawrence]

On 14/06/2010 15:02, madhuri vio wrote:

i have tried this still unable to get an output

from Bio import Seq
from Bio import SeqIO
from Bio import SeqRecord

for seq_record in SeqIO.read("ls_MTbH37Rv.fasta", "fasta"):
     print seq_record.id
     print repr(seq_record.seq)
     print len(seq_record)

python bio.py
Traceback (most recent call last):
   File "bio.py", line 10, in<module>
     for seq_record in SeqIO.read("ls_MTbH37Rv.fasta", "fasta"):
   File "/var/lib/python-support/python2.6/Bio/SeqIO/__init__.py", line 433,
in read
     iterator = parse(handle, format, alphabet)
   File "/var/lib/python-support/python2.6/Bio/SeqIO/__init__.py", line 342,
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)

Please read this, it'll show you your mistake.

http://www.biopython.org/wiki/SeqIO#Sequence_Input

Regards.

Mark Lawrence.

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