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Incorrect contig taxonomy while converting a GTO into a GenBank with rast-export-genome #13

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pdec opened this issue Feb 16, 2021 · 0 comments

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@pdec
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pdec commented Feb 16, 2021

Hi,

I noticed that when a GTO file is converted into a GenBank one with rast-export-genome, SOURCE and ORGANISM fields are corrupted. Here's an example:

genome_id: 1396.2510
in GTO file there's a part:

"close_genomes" : [],
"domain" : "Bacteria",
"taxonomy" : [
"cellular organisms",
"Bacteria",
"Terrabacteria group",
"Firmicutes",
"Bacilli",
"Bacillales",
"Bacillaceae",
"Bacillus",
"Bacillus cereus group",
"Bacillus cereus"
],
(...)

and when converted to GenBank, there's:

SOURCE ARRAY(0x35df9e0)
ORGANISM ARRAY(0x35df9e0)
.

although it should look like that:

SOURCE Bacillus cereus strain ET31
ORGANISM Bacillus cereus strain ET31
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus; Bacillus cereus group; Bacillus cereus.

It would be great if you could fix that, thanks!

Best,
Przemek

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