> 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
Peter, 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. J. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
