[Biopython-dev] Notification: incoming/56

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chapmanb changed notes

Message summary for PR#56
	From: rree at ucdavis.edu
	Subject: GenBank parser
	Date: Wed, 30 Jan 2002 18:29:11 -0500
	0 replies 	0 followups
	Notes: Thanks Rick. I actually just fixed this bug this morning :-). Your fix is
basically identical to mine. Thanks for the report; those sneaky fellas at NCBI
got another change by me!



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>From rree at ucdavis.edu Wed Jan 30 18:29:12 2002
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Date: Wed, 30 Jan 2002 18:29:11 -0500
Message-Id: <200201302329.g0UNTBit023912 at pw600a.bioperl.org>
From: rree at ucdavis.edu
To: biopython-bugs at bioperl.org
Subject: GenBank parser

Full_Name: Rick Ree
Module: GenBank/genbank_format.py
Version: CVS 1.16
OS: Linux
Submission from: loco.ucdavis.edu (169.237.66.27)


Genbank parser was choking on the plant flat files from NCBI's ftp site -- on
the LOCUS line of the record, the parser was expecting 'circular' where my file
had 'linear'.  Here is a diff that fixes the problem, but the formatting is all
wonky 'cos of this HTML form, sorry.

-Rick

Index: genbank_format.py
===================================================================
RCS file: /home/repository/biopython/biopython/Bio/GenBank/genbank_format.py,v
retrieving revision 1.16
diff -u -r1.16 genbank_format.py
--- genbank_format.py	5 Jan 2002 22:09:58 -0000	1.16
+++ genbank_format.py	30 Jan 2002 23:31:47 -0000
@@ -106,7 +106,10 @@
                             Martel.Opt(Martel.Alt(*residue_prefixes)) +
                             Martel.Opt(Martel.Alt(*residue_types)) +
                             Martel.Opt(Martel.Opt(blank_space) + 
-                                       Martel.Str("circular")))
+                                       Martel.Str("circular")) +
+                            Martel.Opt(Martel.Opt(blank_space) + 
+                                       Martel.Str("linear"))
+                            )
 
 date = Martel.Group("date",
                     Martel.Re("[-\w]+"))