remote_feature - allele_tower

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remote_feature - allele_tower

Keiran Raine

I'm trying to use the allele_tower feature type to generate the histogram style image via a remote feature.

Previously I was doing this from a database and was getting good results via callbacks, but these don't work with remote features.  I've tried to use the documentation of allele_tower but I'm not sure it is up to date.

Here is an example of my gff3 returned via a cgi script:
##gff-version 3
19	sub	called	2109280	2109280	.	+	.	Name=PD3849a;Alleles=A;Alleles=C;minor_allele=C;maf=0.16
19	sub	called	2514984	2514984	.	+	.	Name=PD3849a;Alleles=A;Alleles=G;minor_allele=G;maf=0.19
previously I would have gained an image like the one attached:

At the moment I seem to get a generic glyph  If I define Alleles, minor_allele and maf as described here I get the following errors in my logs:

Alleles A does not have a value at GFF3 file line 2
Alleles C does not have a value at GFF3 file line 2
minor_allele C does not have a value at GFF3 file line 2
maf 0.2 does not have a value at GFF3 file line 2

Should I be able to get this to work, has anyone else?


Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 2100

-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

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