Hi, George.
I'm really interesting to apply pharokka to my datasets.
Thank you for your great work.
While applying Pharokka to genomes within PhageScope, I discovered that tools like ARAGORN occasionally report negative locations.
Pharokka itself functions without any problems, but errors occur when applying Pharokka's output to subsequent tools such as Phold.
When parsing gbk files using Biopython's SeqIO, if a location has a negative value, it is treated as None.
When reporting this object using .format("gb"), an error occurs if there is a feature with a location of None.
Handling this using CompoundLocation or similar methods should prevent problems when reading the gbk file with Biopython later.
The following is an example of a genome where this issue occurs:
SAMN11031375_a1_ct32534_vs1
SAMN11031375_a1_ct32534_vs1.fna.zip
Hi, George.
I'm really interesting to apply pharokka to my datasets.
Thank you for your great work.
While applying Pharokka to genomes within PhageScope, I discovered that tools like ARAGORN occasionally report negative locations.
Pharokka itself functions without any problems, but errors occur when applying Pharokka's output to subsequent tools such as Phold.
When parsing gbk files using Biopython's SeqIO, if a location has a negative value, it is treated as None.
When reporting this object using
.format("gb"), an error occurs if there is a feature with a location of None.Handling this using CompoundLocation or similar methods should prevent problems when reading the gbk file with Biopython later.
The following is an example of a genome where this issue occurs:
SAMN11031375_a1_ct32534_vs1SAMN11031375_a1_ct32534_vs1.fna.zip