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pangenome / odgi

Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
https://doi.org/10.1093/bioinformatics/btac308
MIT License
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Extending a region with edges! #515

Open coevolutionlab opened 1 year ago

coevolutionlab commented 1 year ago

Hi @AndreaGuarracino and @ekg , Many thanks for developing "odgi"!!

I needed suggestions on the following problem, and if you could provide some answers, that would be super helpful.

  1. I am interested in a region X of my pan-genome graph.
  2. I have identified the nodes in this region.
  3. I want to extend the region X left and right until all the nodes in the original region X have a connecting node (in left and right direction)

Is it even feasible with the current Odgi set of tools ? Apologies if my issue sounds ridiculous. If this is doable, could you please suggest a way (combination of tools)?

Thanks!! best, Gautam

ekg commented 1 year ago

My experience has been that it's easy to collect the path ranges in the subgraph and expand these using the range arithmetic that is implied by what you've described. You could do this with awk and bedtools. Then you use the new targets to extract a new subgraph.

On Fri, Jun 23, 2023, 09:16 coevolutionlab @.***> wrote:

Hi @AndreaGuarracino https://github.com/AndreaGuarracino and @ekg https://github.com/ekg , Many thanks for developing "odgi"!!

I needed suggestions on the following problem, and if you could provide some answers, that would be super helpful.

  1. I am interested in a region X of my pan-genome graph.
  2. I have identified the nodes in this region.
  3. I want to extend the region X left and right until all the nodes in the original region X have a connecting node (in left and right direction)

Is it even feasible with the current Odgi set of tools ? Apologies if my issue sounds ridiculous. If this is doable, could you please suggest a way (combination of tools)?

Thanks!! best, Gautam

— Reply to this email directly, view it on GitHub https://github.com/pangenome/odgi/issues/515, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABDQEORSM5VRBJVPOWZG2TXMU7EFANCNFSM6AAAAAAZRFXTXI . You are receiving this because you were mentioned.Message ID: @.***>

subwaystation commented 1 year ago

Did you solve this @coevolutionlab?