How to join multiple vg files

[RenzoTale88]

Hello,
I've got a very simple question. I've got multiple vg files generated from single chromosome cactus alignments. I would like to combine them in a single vg archive so to process it separately.

Is it ok if I proceed as follow:

for n in {1..N}; do
    vg ids -s GRAPH/chr${n}.tmp.vg > GRAPH/chr${n}.final.vg
done

vg ids -j  $(for i in $(seq 1 n); do echo chr${i}.final.vg; done)

vg join $(for i in $(seq 1 n); do echo chr${i}.final.vg; done) > all.vg

Is it correct?

Thank you again for your help,
Andrea

[ekg]

We really need to remove vg join because it does not do what users expect! It links the graphs to a single head node, and was used during testing I did five years ago. This is getting urgent because we are having one to two support requests a week about this. It used to be that we used vg ids to make the id space of each graph not overlap the others and then just use `cat` to write them into a single graph. I think this still works. vg ids -j a.vg b.vg c.vg cat a.vg b.vg c.vg >x.vg

…

On Tue, Oct 22, 2019, 11:19 RenzoTale88 ***@***.***> wrote: Hello, I've got a very simple question. I've got multiple vg files generated from single chromosome cactus alignments. I would like to combine them in a single vg archive so to process it separately. Is it ok if I proceed as follow: for n in {1..N}; do vg ids -s GRAPH/chr${n}.tmp.vg > GRAPH/chr${n}.final.vg done vg ids -j $(for i in $(seq 1 n); do echo chr${i}.final.vg; done) vg join $(for i in $(seq 1 n); do echo chr${i}.final.vg; done) > all.vg Is it correct? Thank you again for your help, Andrea — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2515?email_source=notifications&email_token=AABDQEMBDRXIEIRODWPLWSTQP3HSJA5CNFSM4JDNSFUKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HTOQ6FQ>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDQEMN7RFYDXYCQ6TF5ODQP3HSJANCNFSM4JDNSFUA> .

[RenzoTale88]

Oh wow, that's even easier!
Thank you for the quick reply and support,

Andrea

[glennhickey]

Agreed on removing vg join. And a vote for removing vg concat for the same reasons.

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On Tue, Oct 22, 2019 at 6:46 AM RenzoTale88 ***@***.***> wrote: Oh wow, that's even easier! Thank you for the quick reply and support, Andrea — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2515?email_source=notifications&email_token=AAG373VRBIEMETOM7OGTQLLQP3KXBA5CNFSM4JDNSFUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEB5JGPA#issuecomment-544903996>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG373TH5WPCRV5XX6NHIP3QP3KXBANCNFSM4JDNSFUA> .