[Bioperl-l] Bio::Search::HSP::FastaHSP -> get_aln -> Bio::Locatable end is float

[Mark A. Jensen]

Hi Alexie--
I am either responsible for this weirdness, or have fixed it in
an unreleased version. Anyway,  can you please make a bug
report at http://bugzilla.bioperl.org, and include some relevant
code and real data, and I will have a look.
Thanks a lot- Mark
----- Original Message ----- 
From: "Alexie Papanicolaou" <alpapan at googlemail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Thursday, September 10, 2009 5:14 PM
Subject: [Bioperl-l] Bio::Search::HSP::FastaHSP -> get_aln -> Bio::Locatable end 
is float


> Hello all,
>
> I get the following warning when parsing a fasty34 HSP using Bio::Search
> and then trying to getting the alignment using get_aln
>
> MSG: In sequence CONTIG residue count gives end value
> 565.333333333333.
> Overriding value [565] with value 565.333333333333 for
> Bio::LocatableSeq::end().
> MAEMFKIGDLVWAKMKGFSPWPGLVSNPTKDLKRPTSKKSAQQ/C/VFFLGTNNYAWIEEANIKPYFEYRDRLVKSNKSGAFKDALDAIEEYIKNNGAKFDDPDAEFNRLRESLAEKKESKPKQRKEKRPAHDDNSAKSPKKVRTNSVEADKESVRADSPILSNHSPRKGPASTLLERPTTIVRPLDDSQD
> STACK
> Bio::LocatableSeq::end /usr/local/share/perl/5.8.8/Bio/LocatableSeq.pm:196
> STACK
> Bio::LocatableSeq::new /usr/local/share/perl/5.8.8/Bio/LocatableSeq.pm:140
> STACK
> Bio::Search::HSP::FastaHSP::get_aln 
> /usr/local/share/perl/5.8.8/Bio/Search/HSP/FastaHSP.pm:174
>
> The frameshifts (/ and \ ) are causing this recalculation of length to a
> float (which is a bit weird) but is not fatal for my program. Is this
> intentional?
>
> My immediate problems is actually the warning message itself - which is
> quite annoying if you have hundreds of such sequences... any way to turn
> them off sort of commenting out the line at LocatableSeq.pm ?
> (redirecting STDERR wouldn't be desirable for a production script).
>
> many thanks
> alexie
>
>
> -- 
> Alexie Papanicolaou
> Richard ffrench-Constant group
> CEC-Biology
> Univ. Exeter in Cornwall
> Penryn
> TR10 9EZ
> United Kingdom
>
>
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