> Sorry -more questions - could you explain what the "Interpret features
> when possible" setting in the "Extract Genomic DNA" is meant to do?
> The tool's help text doesn't say anything (other than it is only for
> GTF/GFF files).
> In the NC_005213.1 example turning "Interpret features when possible"
> on seems to massively collapse down the number of features. I'm not
> sure what is happening but suspect this is in part down to the NCBI
> GFF3 file being broken with regards to the lack of any ID tags? See also:
> http://blastedbio.blogspot.com/2011/08/why-are-ncbi-gff3-files-still-broken.html


Interpret features means that the GFF parser aggregates features for a single 
parent feature (i.e. does multi-line parsing), extracts the sequences for each 
child feature, and creates the sequence for the parent by concatenating the 
child features' sequences.

Yes, this needs to be better documented.

> And on another issue, looking at the code for extract_genomic_dna.py
> there appears to be no attempt to support circular genomes with features
> wrapping the origin.

Correct, this is not implemented.

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