[Biopython-dev] Notification: incoming/39

biopython-bugs at bioperl.org biopython-bugs at bioperl.org
Tue Aug 14 02:10:10 EDT 2001

JitterBug notification

jchang moved PR#39 from incoming to fixed-bugs
Message summary for PR#39
	From: cirano at chollian.net
	Subject: Parsing Problem of GenBank format
	Date: Mon, 13 Aug 2001 21:57:23 -0400
	0 replies 	0 followups
	Notes: Thanks for the bug report.  Andrew Dalke noted this earlier and submitted the
follow fix for UndoHandle.read:
   def read(self, size=-1):
        if size == -1:
            saved = string.join(self._saved, "")
            self._saved[:] = []

It's checked into the CVS and will go out the next release.  Actually, enough
people are getting tripped out on it that that should happen sooner than later.


>From cirano at chollian.net Mon Aug 13 21:57:24 2001
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Date: Mon, 13 Aug 2001 21:57:23 -0400
Message-Id: <200108140157.f7E1vIq28563 at pw600a.bioperl.org>
From: cirano at chollian.net
To: biopython-bugs at bioperl.org
Subject: Parsing Problem of GenBank format

Full_Name: Chang Gyeom, Kim
Module: Bio/File.py/saveline module
Version: Biopython1.00a2
OS: Redhat7.1
Submission from: (NULL) (

My Source code:  

	from Bio import GenBank

	search_term = "Lupine leghemoglobin"

	gi_list = GenBank.search_for(search_term)

	ncbi_dict = GenBank.NCBIDictionary()
	gb_seqrecord = ncbi_dict[ gi_list[0] ]
	print gb_seqrecord

When I run this code, I lost first 5 lines of GenBank Record.
I think this problem is caused by the function of "saveline" 
located in Bio/File.py module

So I revised the code like this:

    def saveline(self, line):
        if line:
            handle_contents = self.read()
            self._saved = line + handle_contents
            self._handle = StringIO.StringIO(self._saved)

Although I fixed my problem, I'm not sure this is the right way.

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