[Bioperl-l] Fwd: [Bug 1365] load_seqdatabase.pl fails when LOCUS name contains a space

[Hilmar Lapp]

I know, encountered this before myself. The problem is that the genbank 
parser
in this case erroneously assigns the second part of the LOCUS name to 
the
sequence length, which doesn't bother Bio::Seq, but does bother the 
RDBMS
because the length is declared as a numeric type.

So, the problem is either with the genbank parser, or with the record 
itself. When I had this problem and checked the input (is it RefSeq?), 
there was only once single such record. I thought that one also had 
been fixed in a subsequent release, but I'm not sure. I'm not sure NCBI 
allows spaces in the LOCUS ID (which becomes the display_id). Can 
anyone try to confirm whether this is valid syntax and if not, whether 
the problem has been fixed in a later release?

     -hilmar

Begin forwarded message:

> From: bugzilla-daemon@cvs.open-bio.org
> Date: Wed Jan 15, 2003  1:34:44  PM US/Pacific
> To: hlapp@gnf.org
> Subject: [Bug 1365] New: load_seqdatabase.pl fails when LOCUS name 
> contains a space
>
> http://bugzilla.bioperl.org/show_bug.cgi?id=1365
>
>            Summary: load_seqdatabase.pl fails when LOCUS name contains 
> a
>                     space
>            Product: Bioperl
>            Version: 1.2 branch
>           Platform: SGI
>         OS/Version: IRIX
>             Status: NEW
>           Severity: normal
>           Priority: P2
>          Component: Biosql
>         AssignedTo: hlapp@gnf.org
>         ReportedBy: limje@bms.com
>
>
> Unable to load a RefSeq record where the LOCUS line has the following 
> format:
>
> LOCUS       Arf GAP1                1862 bp    mRNA    linear   ROD 
> 13-JAN-2003
>
> The error message I get (SGI/IRix/PostgreSQL 7.2.1)is as follows:
> DBD::Pg::st execute failed: ERROR: pg_atoi: error in "GAP1": can't 
> parse "GAP1"
> at <path_name>/Bio/DB/BioSQL/BaseDriver.pm line 564, <GENO> line 
> 171708.
>
>
>
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>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------