[ensembl-dev] unable to recover high-r2 pair using fetch_by_VariationFeatures

Anja Thormann anja at ebi.ac.uk
Mon Apr 24 13:18:26 BST 2017


Hi Andrew,

both is now fixed on the release/88 branch. Please refresh the code.

Thank you,
Anja

> On 20 Apr 2017, at 17:30, andrew126 at mac.com wrote:
> 
> Hi Anja,
> 
> Thanks for the response.
> 
> I’ve installed API 88 and things seem to work so far (the expected r2 value is returned .. smile), with the following observations:
> 
> 1)
> Running my code now generates looooots of these messages (regardless of if I use remote or local vcfs):
> 
> 	Use of uninitialized value in hash element at /home/andrew/gte/src_88/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm line 488.
> 
> This is the offending line:
> 	$synonyms{$syn->[0]} = $sample->name;
> 
> I presume these are benign messages?
> 
> 2)
> ensemble-variation/C_code/ld_vcf.c wanted:
> 	return 0;
> at the end of main().
> 
> Thanks for the help.
> 
> Best,
> 
> Andrew
> 
> 
>> On Apr 20, 2017, at 1:51 AM, Anja Thormann <anja at ebi.ac.uk> wrote:
>> 
>> Hi Andrew,
>> 
>> we had problems with fetch_by_VariationFeatures for that release. Would it be possible for you to use the most recent version 88 of our API?
>> 
>> Thank you,
>> Anja
>>> On 17 Apr 2017, at 05:56, andrew126 at mac.com wrote:
>>> 
>>> Hi,
>>> 
>>> I am using API version 86.
>>> 
>>> There are two snps within 1kb of each other that have a high r2 value:
>>> 
>>> rs79796976 (chr1, pos 247,390,677)
>>> rs56285508 (chr1, pos 247,391,186)
>>> r^2 0.983802 in 1000GENOMES:phase_3:EUR
>>> 
>>> I can recover rs56285508 as a high-LD pair when I use fetch_by_VariationFeature (no “s” at the end), querying with rs79796976.
>>> 
>>> However, I get no result when I use fetch_by_VariationFeatures (with an “s” at the end), querying with both snps.
>>> 
>>> Below is the perl script using fetch_by_VariationFeatures.
>>> 
>>> Can you please let me know if I am using fetch_by_VarationFeatures incorrectly?
>>> 
>>> Thanks for any guidance.
>>> 
>>> Best regards,
>>> 
>>> Andrew
>>> 
>>> 
>>> 
>>> use strict;
>>> $|=1;
>>> use IPC::Run;
>>> use Bio::EnsEMBL::Registry;
>>> use Bio::EnsEMBL::ApiVersion; 
>>> printf( "The API version used is %s\n", software_version() ); 
>>> 
>>> my $registry = 'Bio::EnsEMBL::Registry';
>>> $registry->load_all();
>>> $registry->set_reconnect_when_lost(1);
>>> $registry->load_registry_from_db(
>>>  -host => 'ensembldb.ensembl.org', # alternatively ensembldb 'useastdb.ensembl.org'
>>>  -user => 'anonymous'
>>>  );
>>> 
>>> my $chrom = "1";
>>> my $var1 = "rs79796976";
>>> my $region_start1 = "247390677";
>>> my $region_end1 = "247390677";
>>> my $var2 = "rs56285508";
>>> my $region_start2 = "247391186";
>>> my $region_end2 = "247391186";
>>> 
>>> my $pop_adaptor = $registry->get_adaptor("human","variation","population");
>>> $pop_adaptor->db->use_vcf(1);
>>> my $ldFeatureContainerAdaptor = $registry->get_adaptor('human', 'variation', 'ldfeaturecontainer');
>>> $ldFeatureContainerAdaptor->db->use_vcf(1);
>>> my $variation_adaptor = $registry->get_adaptor( 'human', 'variation', 'variation' );
>>> $variation_adaptor->db->use_vcf(1);
>>> 	
>>> my $population_name = "1000GENOMES:phase_3:EUR";
>>> my $population = $pop_adaptor->fetch_by_name($population_name);
>>> 	
>>> my $variation1 = $variation_adaptor->fetch_by_name("$var1");
>>> my $vfref1 = $variation1->get_all_VariationFeatures();
>>> my $query_variation_feature1;
>>> my $found=0;
>>> foreach my $vf1 (@{$vfref1}) {
>>>  if ($chrom eq $vf1->seq_region_name) {
>>> 	if ($region_start1 eq $vf1->seq_region_start && $region_end1 eq $vf1->seq_region_end) {
>>> 	    $found=1;
>>> 	    $query_variation_feature1 = $vf1;
>>> 	}
>>>  }
>>> }
>>> if ($found==0) {die;}
>>> 
>>> my $variation2 = $variation_adaptor->fetch_by_name("$var2");
>>> my $vfref2 = $variation2->get_all_VariationFeatures();
>>> my $query_variation_feature2;
>>> $found=0;
>>> foreach my $vf2 (@{$vfref2}) {
>>>  if ($chrom eq $vf2->seq_region_name) {
>>> 	if ($region_start2 eq $vf2->seq_region_start && $region_end2 eq $vf2->seq_region_end) {
>>> 	    $found=1;
>>> 	    $query_variation_feature2 = $vf2;
>>> 	}
>>>  }
>>> }
>>> if ($found==0) {die;}
>>> 
>>> my $ldFeatureContainer = $ldFeatureContainerAdaptor->fetch_by_VariationFeatures([$query_variation_feature1, $query_variation_feature2],$population);
>>> 
>>> foreach my $r_square (@{$ldFeatureContainer->get_all_r_square_values}){
>>>  if ($r_square->{r2} >= 0.1){ 
>>> 	print $r_square->{variation1}->variation_name."\n";
>>> 	print "\t".$r_square->{variation1}->seq_region_start."\n";
>>> 	print "\t".$r_square->{variation1}->seq_region_end."\n";
>>> 	print $r_square->{variation2}->variation_name."\n";
>>> 	print "\t".$r_square->{variation2}->seq_region_start."\n";
>>> 	print "\t".$r_square->{variation2}->seq_region_end."\n";
>>> 	print "r^2 ".$r_square->{r2}."\n";
>>>  }
>>> }
>>> 
>>> 
>>> 
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