shorter than real intergenic space in "report_gff_intron_and_intergenic_stats.py" about biocode HOT 4 CLOSED

At first I wasn't sure what to do here, so I turned to the definition of intergenic_region from the Sequence Ontology:

http://www.sequenceontology.org/browser/current_svn/term/SO:0000605
"A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome."

Based on this, yes, the ends of the contigs to the proximal gene should be included as intergenic space. I can make this change, but it would still mean that short contigs with no annotated genes would NOT be added. Do you agree?

from biocode.

Hi,

Yes I agree. If one want to have short contigs with no gene, they should
calculate it separately.

Thanks,
Pezhman

On Sat, Jun 21, 2014 at 9:24 PM, Joshua Orvis [email protected]
wrote:

At first I wasn't sure what to do here, so I turned to the definition of
intergenic_region from the Sequence Ontology:

http://www.sequenceontology.org/browser/current_svn/term/SO:0000605
"A region containing or overlapping no genes that is bounded on either
side by a gene, or bounded by a gene and the end of the chromosome."

Based on this, yes, the ends of the contigs to the proximal gene should be
included as intergenic space. I can make this change, but it would still
mean that short contigs with no annotated genes would NOT be added. Do you
agree?

Reply to this email directly or view it on GitHub
#18 (comment).

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My apologies, I forgot to update here. About a week ago I committed a version that fixes this, but it currently requires your FASTA data to be embedded at the end of your GFF3 file (per the specification.) Marking this as closed since it fixes the issue, but I'm also adding a --fasta option which will allow it to be in a separate file.

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New version with --fasta now committed.

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