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.