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russelldurrett / gtf-to-genes

Automatically exported from code.google.com/p/gtf-to-genes
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start/beg off by -1? #3

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
It appears that start/beg is off by -1. To use the NNAT example from the page:

http://gtf-to-genes.googlecode.com/hg/doc/build/html/index.html

The GFF entry is for the start codon is:

start_codon 36149734    36149736

GFF is 1 based, you are 0-based, so it should be 36149734-1 = 36149733 but it 
is:

    'start_codons'                : ((36149732, 36149736),),

Elsewhere on the page, you state that length = end - beg

This gives the length of the start_codon as 36149736-36149732 = 4 (while a 
codon = 3 bases)

Original issue reported on code.google.com by davm...@gmail.com on 24 Feb 2013 at 9:42