[BioPython] GenBank parser X automate retrival from gi list

Alexandre dos Santos Cristino alexsc at rge.fmrp.usp.br
Fri Feb 13 16:19:19 EST 2004


 Hello everybody,

 The BioPython project seems to be a very useful tool to bioinformatic
tasks, so congratulations for this initiative!

 I've used GenBank parser as described in the tutorials (with opened
files), but I've failed to use it to process each gi list element.
I'm afraid the parser can't work this way. Is there another solution to do
it? (traceback below)

 thank you!
 alex

ps: I hope help you in this wonderful project, but I need to learn much
more about Python.

Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "searchGeneNCBI.py", line 46, in ?
    resume_seq = gb_parser(gb_record)
  File "/home/alex/anotacao/rot.py", line 5, in gb_parser
    iterator = GenBank.Iterator(gb_record,parser)
  File
"/usr/local/biopython-1.23/build/lib.linux-i686-2.3/Bio/GenBank/__init__.py",
line 126, in __init__
    while _handle.peekline() and _handle.peekline().find("LOCUS") < 0:
  File "/usr/local/biopython-1.23/build/lib.linux-i686-2.3/Bio/File.py",
line 72, in peekline
    line = self._handle.readline()
AttributeError: 'str' object has no attribute 'readline'


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