[Bioperl-l] GFF3loader and indexing

Chris Fields cjfields at uiuc.edu
Fri Nov 9 12:58:16 EST 2007


Quick question: shouldn't the new Index attribute be passed on to  
seqfeatures by DB::SeqFeature::Store::GFF3Loader for round-tripping  
purposes (for instance, properly reloading dumped gff3 data)?  I'm  
testing out a feature editor using volvox.gff3 data in GBrowse and  
the mRNA features appear to drop this attribute once loaded:

Original data:

ctgA	example	gene	1050	9000	.	+	.	ID=EDEN;Name=EDEN;Note=protein kinase
ctgA	example	mRNA	1050	9000	.	+	.	ID=EDEN.1;Parent=EDEN;Name=EDEN. 
1;Note=Eden splice form 1;Index=1
ctgA	example	five_prime_UTR	1050	1200	.	+	.	Parent=EDEN.1

partial gff3_string(1) output:

ctgA	example	gene	1050	9000	.	+	.	 
Name=EDEN;ID=50;Alias=EDEN;Note=protein kinase
ctgA	example	mRNA	1050	9000	.	+	.	Name=EDEN. 
1;Parent=50;ID=51;Alias=EDEN.1;Note=Eden splice form 1
ctgA	example	five_prime_UTR	1050	1200	.	+	.	Parent=51;ID=52
...

chris


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