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althonos / pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
https://pyrodigal.readthedocs.org
GNU General Public License v3.0
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Duplicate extraction of edge nodes on genomes with a start codon on edge #22

Closed althonos closed 1 year ago

althonos commented 1 year ago

Issue seen with a Bifidobacterium genome while debugging #21 : it seems that in closed=False mode, the node extraction produces a duplicate node if there is a start node at the edge of the sequence (ATG in 5' in here):

<pyrodigal._pyrodigal.Node index=0 strand=+1 type='ATG' edge=False>
<pyrodigal._pyrodigal.Node index=0 strand=+1 type='ATG' edge=True>
....

The duplicate node on edge is not being produced by Prodigal, which only emits the non-edge node.

althonos commented 1 year ago

Fixed in e32d155ae6c9b3ddb8963c07cdb4c9e4698875d1.