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

Open pdec opened 3 years ago

pdec commented 3 years ago

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