[Biopython-dev] [Bug 1762] Bio.GenBank.FeatureParser dislikes valid accessions and locus lines

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Nov 9 10:49:25 EST 2005


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
 Attachment #202 is|0                           |1
           obsolete|                            |

------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2005-11-09 10:49 -------
Created an attachment (id=247)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=247&action=view)
Patch to Bio/GenBank/__init__.py

Patch to my non-martel GenBank parser to:

(1) tackle the truncated LOCUS line problem (i.e. this bug)

Plus a few changes that should be on bug 1899 really:

(2) started to split the feed function into sub functions
(3) minor changes to comments to remove references to Martel
(4) removed the ErrorParser class used by the Martel parser

Patch created with:

diff cvs__init__.py __init__.py > patch.txt

test_GenBank.py still passes (only tested on Windows).

Sample output from the test script posted earlier, this time the truncated
LOCUS line is accepted:

Starting... Done
1 U00096 8877 4639675
Starting... Done
Time elapsed 48.34 seconds for c:\temp\U00096_full_locus.gbk
Starting... Done
1 U00096 8877 4639675
Starting... Done
Time elapsed 49.01 seconds for c:\temp\U00096_truncated_locus.gbk

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