Hi there,

I have a GFF3 file where each mRNA is descendent from a single gene, even if they overlap entirely. Example below:

I'd like to merge the these separate mRNAs so that that have the same parent gene (but both mRNAs are independently maintained), and so the gene is possibly renamed based on genomic location (e.g. monotonically increasing gene id based on the number of genes starting from the left most gene). Does anyone know a script that exists to do this? Ideally the script would consider a few different cases, such as

1. Genes that overlap entirely, with a lot of overlap at the exonic level (the example shown above - say exonic overlap > 90% should be merged)
2. Genes which overlap, but only in intronic regions (shouldn't be merged - an example would be a spurious long gene model that bridges two repetative elements that has an "intron" crossing over the 2 mRNAs shown above)