AttributeError: 'DataFrame' object has no attribute 'cumulative'

[subwaystation]

Hi @danydoerr,

I tried to visualize my pangenome-growth output with your Python script, however, I ran into the following problem:

python3 ~/software/panacus/git/master/scripts/visualize_growth.py chrM.hprc-v1.0-pggb.og.pangenome-growth_r100.txt
Traceback (most recent call last):
  File "/home/ubuntu/software/panacus/git/master/scripts/visualize_growth.py", line 66, in <module>
    plot(df, path.basename(args.growth_stats.name), out)
  File "/home/ubuntu/software/panacus/git/master/scripts/visualize_growth.py", line 35, in plot
    plt.bar(x=xticks, height=df.cumulative)
  File "/home/ubuntu/.local/lib/python3.8/site-packages/pandas/core/generic.py", line 5989, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'cumulative'

chrM.hprc-v1.0-pggb.og.pangenome-growth_r100.txt

Thanks for any tips!

[subwaystation]

Both the script and the binary are from today's master.

[danydoerr]

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".

[subwaystation]

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?

[subwaystation]

You also removed the possibility to run several iterations of growth. Was this your intention?

[danydoerr]

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

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!

[danydoerr]

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 :)

[subwaystation]

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

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 <luca.parmigiani@studenti.univr.it>
Date:   Wed May 10 11:45:17 2023 +0200

    intersection and coverage with rug integers

[danydoerr]

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

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 <luca.parmigiani@studenti.univr.it>
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.

[danydoerr]

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

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 <luca.parmigiani@studenti.univr.it>
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.

[subwaystation]

Alright, I am here

commit d77b72d7bbe2837f831e0cc0445c57fcfab8996f (HEAD -> ng, origin/ng)
Author: Dany Doerr <daniel.doerr@hhu.de>
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.

[subwaystation]

Doing all steps from scratch inclusively a fresh clone on my local machine, it worked. Thanks!

[subwaystation]

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 ;)

[danydoerr]

Fixed version is now committed.