[Bioperl-l] bug in location->to_FTstring

[Hilmar Lapp]

The strand bug should be fixed on the main trunk (and hence the 
upcoming 1.2)

As for flattening, call $splitloc->each_Location() (this does NOT 
return the 'top' location object though).

	-hilmar

On Tuesday, December 3, 2002, at 07:00 AM, Philip Lijnzaad wrote:

> Dear all,
>
> hope you're all doing well!  Quick question. I installed 
> bioperl-1.0.2 from
> CPAN, and noticed what looks like a rather serious bug in
>
> Bio::Location (or Bio::Location::Split). When I read the following 
> file:
> ------------------------------------------------------------------------
> ID   foo
> AC   bar
> XX
> FH   Key             Location/Qualifiers
> FH
> FT   gene            complement(1..20)
> FT                   /gene="YJL225C"
> FT   CDS             complement(join(1..4,10..20))
> FT                   /gene="YJL225C"
> SQ   Sequence 60 BP; 15 A; 15 C; 15 G; 15 T; 0 other;
>      cccacacaca caccacaccc acacccacac acaccacacc cacacaccac 
> acccacacca        60
> //
> ------------------------------------------------------------------------
>
> and iterate over the features to extract the locations, like so:
>
>   for my $feat ( $seq->top_SeqFeatures ) {
>   # $feat is a Bio::SeqFeature::Generic
>     print $loc=$feat->location->to_FTstring;
>   }
>
> It prints
>
>   join(1..4,10..20)
>
> which is sort of on the wrong strand. The $feat is a 
> Bio::Location::Split,
> it's splittype is JOIN, it's strand is -1, the strands of the 
> sub_Location is
> 1, so it just looks to_FTstring ignores the strand of the
> Split.
>
> Incidentally, is there a method that 'flattens' the location
> description into something with a nesting depth of at most one (e.g.,
> complement(join(1..4,10..20)) could better be written as
> complement(1..4,10..20)) ? Just wondering. Cheers,
>
>                                                                     
>    Philip
>
> --
> Philip Lijnzaad
> Genomics Laboratory
> Dept. of Biomedical Genetics
> University Medical Center (UMC), Utrecht
> Stratenum, STR 3.223
> room 3.126 (not in on Thursdays)
> P.O. Box 85060, 3508 AB Utrecht
> (Universiteitsweg 100, 3584 CG Utrecht)
> The Netherlands
> tel: +31 (0)30 253 8464
> fax: +31 (0)30 253 9035
>
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--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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