[Bioperl-l] Bio::PopGen::PopStats

[Mark A. Jensen]

Hi Rob, 

Don't forget to 

 use strict;
 use warnings;

There's an omission and a typo in your script that these would have caught. 
You need

 my $stat = Bio::PopGen::PopStats->new()

and 

> my $fst = $stats->Fst(\@pop,\@marker);
should be

my $fst = $stats->Fst(\@pop,\@markers);

cheers MAJ
----- Original Message ----- 
From: "Robin Runyowa" <robrunyowa at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Cc: <robrunyowa at gmail.com>
Sent: Tuesday, October 20, 2009 1:20 PM
Subject: [Bioperl-l] Bio::PopGen::PopStats


> Hi, I am a newbie in bioperl and I am trying to use to
> Bio::PopGen::PopStats.
> Unfortunately, I am not sure how to create arrays of objects so I keep
> getting an error message.
> My input files  are below:
> testpop3.cvs:
> SAMPLE,rs0001
> Person1,A T
> Person2,T T
> Person3,A A
> Person4,T A
> Person5,A A
> 
> 
> testpop4.cvs
> SAMPLE,rs0001
> Per1,A T
> Per2,T T
> Per3,A A
> Per4,T A
> Per5,A A
> 
> 
> My script:
> use Bio::PopGen::PopStats;
> use Bio::PopGen::Individual;
> use Bio::PopGen::Genotype;
> use Bio::PopGen::Population;
> use Bio::PopGen::IO;
> 
> my $handle = new Bio::PopGen::IO (-format => 'csv',
>                                -file => 'testpop3.cvs');
> my $handle2 = new Bio::PopGen::IO (-format => 'csv',
>                                -file => 'testpop4.cvs');
> 
> my $YRI = $handle ->next_population;
> my $CEU = $handle2 ->next_population;
> my @pop = ();
> push @pop, $YRI;
> push @pop, $CEU;
> @markers = $YRI->get_marker_names;
> my $fst = $stats->Fst(\@pop,\@marker);
> 
> Thanks, Rob
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