[Bioperl-l] Re: a bug in the package Bio::Tools::BPlite::Sbjct.

[Jason Stajich]

I applied the fix.

On Tue, 16 Mar 2004, Frederic Pecqueur wrote:

> Hi everybody,
>
> I Found a bug in this package.
> Sometimes, when I use $hsp->nextHSP, the $hsp->query->end value is null.
> I always have this error for the last hit.
>
> I solved the problem.
> You need to change the line 235 by :
>
>       elsif ($_ =~ /^>|^Histogram|^Searching|^Parameters|^\s+Database:|^CPU\stime|^\s*Lambda|^\s*Subset/)
>
> For example, if you look in the array @hspline for the last hit of one entry, you can see :
>
> Query: 41  PATLLMLLLKVNKDGPAKKDIWRAPGNQAQVRKLSQVMQHGRLVNIENFTVYTAASVIKK 100
>            P+ L   L  + K G   + I R   +  +V +  Q  + G+     +   +     IK
> Sbjct: 176 PSFLEKALQFIEKYGTKIEGILRQSADVEEVERRVQEYEQGKTEFTFDEDPHVVGDCIKH 235
> Query: 101 FLSKLPNGIFGRDNEETLFNSASTGMDIEKQRQVFYRIFGSLPVASQHLLVLLFGTFRVV 160
>             L +LP+          L  +        +   +   I  + P  ++ LL  +      +
> Sbjct: 236 VLRELPSSPVSASCCTALLEAYRIESKEARISSLRSAIAETFPEPNRRLLQRILKMMHTI 295
> Query: 161 ADSSDGHSNAMNPNAIAISVAPSL 184
>              SS  H N MNPNA+A  +AP L
> Sbjct: 296 --SSHSHENRMNPNAVAACMAPLL 317
>   Subset of the database(s) listed below
>      Number of letters searched: 46,987,626
>      Number of sequences searched:  126,777
>
> If you add "|^\s*Subset" in the test, you should obtain :
>
> Query: 41  PATLLMLLLKVNKDGPAKKDIWRAPGNQAQVRKLSQVMQHGRLVNIENFTVYTAASVIKK 100
>            P+ L   L  + K G   + I R   +  +V +  Q  + G+     +   +     IK
> Sbjct: 176 PSFLEKALQFIEKYGTKIEGILRQSADVEEVERRVQEYEQGKTEFTFDEDPHVVGDCIKH 235
> Query: 101 FLSKLPNGIFGRDNEETLFNSASTGMDIEKQRQVFYRIFGSLPVASQHLLVLLFGTFRVV 160
>             L +LP+          L  +        +   +   I  + P  ++ LL  +      +
> Sbjct: 236 VLRELPSSPVSASCCTALLEAYRIESKEARISSLRSAIAETFPEPNRRLLQRILKMMHTI 295
> Query: 161 ADSSDGHSNAMNPNAIAISVAPSL 184
>              SS  H N MNPNA+A  +AP L
> Sbjct: 296 --SSHSHENRMNPNAVAACMAPLL 317
>
> I tested, with a large blast report..ans it works.
>
> Best regards.
> Frédéric.
>
> Frédéric PECQUEUR
> BioInformatic team
> Devgen nv
> Technologiepark 30
> B - 9052 Zwijnaarde
> Belgium
> Tel: +32 9 324 24 36
> Fax: +32 9 324 24 25
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu