[Bioperl-l] references in swissprot

Hilmar Lapp hlapp at gnf.org
Tue Dec 14 23:24:18 EST 2004

This is mainly an FYI for those who may be affected. If you are using 
bioperl 1.4 you are not affected.

The SeqIO swissprot parser had a bug in parsing references. 
Specifically, for all except the first reference entry in a sequence, 
authors, location, and title will be wrong in that they concatenated 
the value of the preceding reference with that of the current. If there 
is no value for the current (e.g., no title), then that attribute will 
erroneously have the same value as the preceding reference. This will 
also be the case for start and end position (these won't be 
concatenated though).

The bug was introduced in a version (1.80) after the 1.4 branch. I 
fixed it today, so far only on the main trunk. (I also added tests to 
detect this problem.)

Aaron, do you want me to merge this into the 1.5 rc1 branch, or will 
you still branch the official release off of the main trunk?

Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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