Comments (13)
You also removed the possibility to run several iterations of growth. Was this your intention?
Yes. We compute the growth curve exactly, so no need to sample. And we are faster doing so :)
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Both the script and the binary are from today's master.
from panacus.
Please use the "ng" branch. It's close to being released. We will probably push to main some time next week. Also, if you call visualize_growth.py
, make sure to pipe the output into a file, e.g. "> growth.pdf".
from panacus.
I gave it another try using the ng
branch and now the following command is just stuck and I have to type q
to end it. Control + C
did have no effect:
python3 ~/software/panacus/git/master/scripts/visualize_growth.py chrM.hprc-v1.0-pggb.og.histgrowth.tsv > chrM.hprc-v1.0-pggb.og.histgrowth.tsv.pdf
I did the following to generate the file:
panacus histgrowth -c bps chrM.hprc-v1.0-pggb.gfa > chrM.hprc-v1.0-pggb.og.histgrowth.tsv
Would I need to use another subcommand?
from panacus.
You also removed the possibility to run several iterations of growth. Was this your intention?
from panacus.
I gave it another try using the
ng
branch and now the following command is just stuck and I have to typeq
to end it.Control + C
did have no effect:
python3 ~/software/panacus/git/master/scripts/visualize_growth.py chrM.hprc-v1.0-pggb.og.histgrowth.tsv > chrM.hprc-v1.0-pggb.og.histgrowth.tsv.pdf
Are you running the latest version?
I did the following to generate the file:
panacus histgrowth -c bps chrM.hprc-v1.0-pggb.gfa > chrM.hprc-v1.0-pggb.og.histgrowth.tsv
Would I need to use another subcommand?
That's the right command!
from panacus.
I gave it another try using the
ng
branch and now the following command is just stuck and I have to typeq
to end it.Control + C
did have no effect:python3 ~/software/panacus/git/master/scripts/visualize_growth.py chrM.hprc-v1.0-pggb.og.histgrowth.tsv > chrM.hprc-v1.0-pggb.og.histgrowth.tsv.pdf
Are you running the latest version?
I did the following to generate the file:
panacus histgrowth -c bps chrM.hprc-v1.0-pggb.gfa > chrM.hprc-v1.0-pggb.og.histgrowth.tsv
Would I need to use another subcommand?
That's the right command!
I am using
commit 96776f697b989643056e107d9fba52d10c422653 (HEAD -> ng, origin/ng)
Author: lucaparmigiani <[email protected]>
Date: Wed May 10 11:45:17 2023 +0200
intersection and coverage with rug integers
from panacus.
I gave it another try using the
ng
branch and now the following command is just stuck and I have to typeq
to end it.Control + C
did have no effect:python3 ~/software/panacus/git/master/scripts/visualize_growth.py chrM.hprc-v1.0-pggb.og.histgrowth.tsv > chrM.hprc-v1.0-pggb.og.histgrowth.tsv.pdf
Are you running the latest version?
I did the following to generate the file:
panacus histgrowth -c bps chrM.hprc-v1.0-pggb.gfa > chrM.hprc-v1.0-pggb.og.histgrowth.tsv
Would I need to use another subcommand?
That's the right command!
I am using
commit 96776f697b989643056e107d9fba52d10c422653 (HEAD -> ng, origin/ng) Author: lucaparmigiani <[email protected]> Date: Wed May 10 11:45:17 2023 +0200 intersection and coverage with rug integers
Yeah, this is not the latest version. It's no on d77b72d. Please update.
from panacus.
I gave it another try using the
ng
branch and now the following command is just stuck and I have to typeq
to end it.Control + C
did have no effect:python3 ~/software/panacus/git/master/scripts/visualize_growth.py chrM.hprc-v1.0-pggb.og.histgrowth.tsv > chrM.hprc-v1.0-pggb.og.histgrowth.tsv.pdf
Are you running the latest version?
I did the following to generate the file:
panacus histgrowth -c bps chrM.hprc-v1.0-pggb.gfa > chrM.hprc-v1.0-pggb.og.histgrowth.tsv
Would I need to use another subcommand?
That's the right command!
I am using
commit 96776f697b989643056e107d9fba52d10c422653 (HEAD -> ng, origin/ng) Author: lucaparmigiani <[email protected]> Date: Wed May 10 11:45:17 2023 +0200 intersection and coverage with rug integers
Yeah, this is not the latest version. It's no on d77b72d. Please update.
No need to re-run panacus, just re-run the visualization script.
from panacus.
Alright, I am here
commit d77b72d7bbe2837f831e0cc0445c57fcfab8996f (HEAD -> ng, origin/ng)
Author: Dany Doerr <[email protected]>
Date: Wed May 10 14:21:38 2023 +0200
improve visualization
And I ran
panacus histgrowth -c bps chrM.hprc-v1.0-pggb.gfa > chrM.hprc-v1.0-pggb.og.histgrowth.tsv
python3 ~/software/panacus/git/master/scripts/visualize_growth.py chrM.hprc-v1.0-pggb.og.histgrowth.tsv > chrM.hprc-v1.0-pggb.og.histgrowth.tsv.pdf
Which gives me
Input file "chrM.hprc-v1.0-pggb.og.histgrowth.tsv" has wrong header. It doesn't seem to be generated by panacus, exiting.
from panacus.
Doing all steps from scratch inclusively a fresh clone on my local machine, it worked. Thanks!
from panacus.
Edit: There was indeed a bug within the header of the TSV. It worked only works when you execute via ./target/release/panacus
, but fails when using a symlink running directly panacus
. A fix is incoming I was told ;)
from panacus.
Fixed version is now committed.
from panacus.
Related Issues (20)
- Option to output plots in separate PNG files HOT 11
- Could you please make an new release? HOT 3
- command is not supported for more than 65534 HOT 6
- How to Visualize the results of the minigraph-cactus? HOT 21
- Request software updates HOT 6
- Feature request: Alternative plot with #nodes/#edges vs AC
- A problem while running panacus-visualize HOT 1
- Update Readme to reflect installation of python dependencies in the installation section. HOT 1
- compiler error in rustc-serialize HOT 3
- Haplotype labels in TSV, visualisations ? HOT 8
- panacus-visualize.py is overwhelmed by 1000 haplotypes HOT 10
- how is panacus treating Ns HOT 4
- Discrepancy between graph length, reference length, and novel base pairs HOT 3
- What does the output content represent HOT 7
- could you give us an example of cactus? HOT 7
- Installation instructions HOT 2
- Merge different chroms stats into one graph HOT 3
- path coordinates HOT 8
- After `panacus hist` and `panacus growth`, the final visualization will show `#nodes` instead of `bps`. I use `-c bp` for hist HOT 1
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