[ensembl-dev] GenomicAlignBlock restriction

[Jason Rozick]

Hello Benoit,
Haplotype blocks & Compara, also can check TCP1, t-Complex, chr 6:160 mil,  (-quick UCSC check, has ACA20, 29, and SNORD, then getting in more parent genomics senses like 
BC 000665, ORF mRNA, look for gaps and reasoning).
In initial GAB search.
EBI WIT, re-sequenced sires rs42766480, denoted Protein Yield PY93_(A to E)., D lowest, how to search NM, as here in PMC3171720, NM181008.2, to C/EBP enhancer to CCAAT motifs, Casein, is Kinase and as TF, also (it’s protein tree for, just CM type lactation relevance NRC.gov and direction), P^32_ issues., Bull animal.
Skips, I’ve seen mentioned in association along with “GA” nt., in, DMD, nonsense, NHEJ, repair (), E. Coli., GroEL()., UCSC COSMIC, gaps here, as in (atgc/atgc, also * areas),no full features, is ok, while very specilaized.
I will follow up on these topics, in the next fews hours, 10:15 pm EST now.

--------------------------------------------
On Wed, 7/16/14, Benoît Ballester <benoit.ballester at inserm.fr> wrote:

 Subject: [ensembl-dev] GenomicAlignBlock restriction
 To: "dev" <dev at ensembl.org>
 Date: Wednesday, July 16, 2014, 5:46 PM
 
 Hi Compara/Ensembl, 
 
 I'd like to have confirmations about some of the
 GenomicAlignBlock API logic. 
 
 Given a human slice (300 to 400bp), I want to fetch a GAB to
 see if I could find an alignment across species. I want to
 know if that slice is aligneable in a couple of species. 
 
 
 I use
 $gab_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice to
 fetch the GenomicAlignBlock. 
 
 But this returns the entire GenomicAlign for the given block
 ! Right ? 
 
 
     #-- Get GAB         
                
                
                
                
                
                
                
            
     my $slice =
 $slice_adaptor->fetch_by_region( 'chromosome',
 $seq_region_name, $seq_region_start, $seq_region_end
 );               
   
                
                
                
                
                
        
     my $gabs =
 $gab_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice($mlss,
 $slice);             
                
                
          
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                 
     if (scalar @$gabs > 0){ #-- There is a
 GAB               
                
                
                
                
                
      
                
                
                
                
                
                
                
                
                
     
         foreach my $gab (@$gabs) { 
                
                
                
                
                
                
            
    
           #-- do something 
                
                
                
                
                
                
                
                
         
       # but this will return the entire
 GenomicAlign
     }
      }
 
 
 So, correct me if I am wrong, I can restrict the GAB using
 the method restrict_between_reference_positions giving the
 start/end coordinates  of my initial slice, and the
 boolean $skip_empty_GenomicAligns ? 
 
 
 Once I have the GAB I restrict it : 
 
          my $gab2 =
 $gab->restrict_between_reference_positions($rf->seq_region_start,
 $rf->seq_region_end, undef ,1); 
 
 
 Could you please confirm that what I am doing is correct. 
 I want to do that from a human slice, and find if there is
 an alignment for a couple of species. I want to skip empty
 alignments, or long gaps. If this the correct way ? 
 
 Thanks for the replies, 
 
 
 Ben
 
 
 --
 Benoît Ballester, PhD
 Inserm U1090, TAGC
 Campus de Luminy
 13288 Marseille Cedex 9
 France
 +33 4 91 82 87 39
 
 
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