[Bioperl-l] genomic coordinates always on the plus strand

[Jim Hu]

In BioPerl end( to) is always > start(from) and the strand is indicated by strand.  IIRC, there is a proposal for how to handle this for features that cross the origin in circular genomes, but it hasn't been implemented yet. See:

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Range.html

Jim Hu

On May 4, 2012, at 2:29 PM, Hermann Norpois wrote:

> Hello,
> 
> in the tutorial
> http://www.bioperl.org/wiki/HOWTO:Getting_Genomic_Sequencesthere is a
> script that retrieves genomic coordinates (see below). I tested
> it with 14 geneIDs and got always coordinates on "plus strand" meaning
> $from was always a lower number than $to. Principally this is nice but I
> was surprised. This means that all by genes are (by chance) on the plus
> strand or that there are 2 "coordinates" (one for the "plus" one for the
> "minus" strand). Then it could be possible (theoretically and not very
> likely) that there are two genes for one $from/$to pair (one on the plus
> and one on the minus strand with the same coordinates with different IDs).
> I did not find anything about this issue in the documentation or in the
> archive. Could please anybody comment on this?
> 
> use strict;use Bio::DB::EntrezGene;
> my $id = shift <http://perldoc.perl.org/functions/shift.html> or die
> <http://perldoc.perl.org/functions/die.html> "Id?\n"; # use a Gene id
> my $db = new Bio::DB::EntrezGene;
> my $seq = $db->get_Seq_by_id($id);
> my $ac = $seq->annotation;
> for my $ann ($ac->get_Annotations('dblink')) {
> 	if ($ann->database eq "Evidence Viewer") {
>                # get the sequence identifier, the start, and the stop
> 		my ($contig,$from,$to) = $ann->url =~
> 		  /contig=([^&]+).+from=(\d+)&to=(\d+)/;
> 		print <http://perldoc.perl.org/functions/print.html> "$contig\t$from\t$to\n";
> 	}}
> 
> 
> Thank you
> Hermann Norpois
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=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054